HHsearch 1.5 NAME c9m98E_ FAM FILE c9m98E_ COM /bmm/www/servers/phyre2/HH/hhmake -i c9m98E_.a3m DATE Sat Jan 17 09:55:12 2026 LENG 76 match states, 76 columns in multiple alignment FILT 100 out of 173 sequences passed filter (-id 90 -cov 0 -qid 0 -qsc -20.00 -diff 100) NEFF 4.8 EVD 0.4729 2.6574 SEQ >ss_pred CCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCC >ss_conf 9755521127038999841698447989999999999866652076762146666776769999996297343569 >Consensus xxxxxxxmxxPsidxllxkvdsrYxLVxlAAKRARqixxxxxxxgxxpxvxxxxxxKpvxiALxEIaxGkvxyxxg >c9m98E_ GYDTPLGITNPPIDELLDRVSSKYALVIYAAKRARQINDYYNQLYVGPLVEPGLQEKPLSIALREIHADLLEHTEG >UniRef50_A8VRS5(3-67:137) tRNA pseudouridine synthase B n=2 Tax=Bacillus RepID=A8VRS5_9BACI E=1e-13 s/c=1.19 id=30% cov=84% -------MLKPSIDSLMTKINSKYTLVTISSQRARELRDYPET---ASMTVRSTSPNFVGRALEEIDQEILGY--- >UniRef50_B4DCN8(1-62:73) DNA-directed RNA polymerase, omega subunit n=1 Tax=Chthoniobacter flavus Ellin428 RepID=B4DCN8_9BACT E=0.0007 s/c=0.73 id=32% cov=79% -------MTSSLLEEAFKVIPSQQLLVNVVSKRVRQLTA-----GHRPMVETGPRMGFSDIALKEIIEGKL----- >UniRef50_A3VSF8(1-59:121) DNA-directed RNA polymerase omega subunit n=1 Tax=Parvularcula bermudensis HTCC2503 RepID=A3VSF8_9PROT E=4e-09 s/c=1.06 id=33% cov=72% ------------VEDCIDKVDNRFDLVLLAAHRARLIAA-----GSPVEVERERDKNPVV-ALRELADDKIT---- >UniRef50_Q3YSH8(1-62:138) DNA-directed RNA polymerase subunit omega n=5 Tax=canis group RepID=RPOZ_EHRCJ E=7e-09 s/c=1.00 id=33% cov=76% ------------VEECMGRTNNKFKLVILASQRAHDLNS-----GACPVIKHKNG-KNTVIALKEIAAKQLDVSS- >UniRef50_B1C5R9(4-63:89) Putative uncharacterized protein n=1 Tax=Anaerofustis stercorihominis DSM 17244 RepID=B1C5R9_9FIRM E=8e-09 s/c=1.02 id=34% cov=80% -------MINPPINELLEKVDNKYVLAMLVAKRSRELFD-----GDEPMVDEYFVN-LITTAVEEVYEDRIGY--- >UniRef50_C1XXM7(1-73:108) DNA-directed RNA polymerase, omega subunit n=2 Tax=Meiothermus RepID=C1XXM7_9DEIN E=5e-06 s/c=0.72 id=34% cov=86% -------MAEPGIDTLLTVTDSKYRLTVVVAKRAQQLLRYQFkntvlEPSEWPKMRTLEGEKpdpnPVTWAMQELRTGRL----- >UniRef50_C2D6B7(13-88:107) Putative uncharacterized protein n=1 Tax=Atopobium vaginae DSM 15829 RepID=C2D6B7_9ACTN E=2e-05 s/c=0.66 id=30% cov=88% -------ITKPEINSLLEKTeENPFLLCAIAAKRACDIKSMIRGQHLRVaaindidTITTEVSGKdPVSAAMNEIDSGDLSY--- >UniRef50_C7HU46(1-62:62) DNA-directed RNA polymerase subunit omega (RNA polymerase omega subunit) n=4 Tax=Clostridiales Family XI. Incertae Sedis RepID=C7HU46_9FIRM E=2e-09 s/c=1.02 id=35% cov=83% -------MNNPSFKELSEISSSRYEICMMAAKRARRIVNGSD------LLTKEVEDKPVTQALHEIMEGKVEKND- >UniRef50_C3WM64(8-70:73) DNA-directed RNA polymerase subunit omega n=15 Tax=Fusobacterium RepID=C3WM64_9FUSO E=1e-05 s/c=0.81 id=28% cov=80% -------------DELLSKIPNKYILTIVCGERARERAKERMERNGEPLPLTKYDKKDTEMkkVFKEILAGKVGY--- # NULL 3706 5728 4211 4064 4839 3729 4763 4308 4069 3323 5509 4640 4464 4937 4285 4423 3815 3783 6325 4665 HMM A C D E F G H I K L M N P Q R S T V W Y M->M M->I M->D I->M I->I D->M D->D Neff Neff_I Neff_D 0 * * 0 * 0 * * * * G 1 * * * * * 0 * * * * * * * * * * * * * * 1 0 * * * * * * 1000 0 0 Y 2 * * * * * * * * * * * * * * * * * * * 0 2 0 * * * * * * 1000 0 0 D 3 * * 1611 572 * * * * * * * * * * * * * * * * 3 0 * * * * * * 1789 0 0 T 4 1135 * * * * * * * * * * * * * 1695 * 2084 * * * 4 0 * * * * * * 2203 0 0 P 5 3000 * * * * 2528 * * * * * * 511 * * * * * * * 5 0 * * * * * * 2203 0 0 L 6 2713 * * 990 * * * * * 3407 * * * * 2766 * 3282 * * * 6 0 * * * * * * 2433 0 0 G 7 * * * * * 1221 * * * * * * * * * 808 * * * * 7 0 * * * * * * 3201 0 0 I 8 * * * * * * * 2473 * 2475 760 * * * * * * 4335 * * 8 0 * * * * * * 4401 0 0 T 9 3764 * * * * * * 1910 * 2048 3981 3650 * * * 4883 2456 4074 * * 9 0 * * * * * * 4436 0 0 N 10 * * 3525 2528 5815 * * * 2831 * * 1735 * * 4096 3318 * * * 3031 10 0 * * * * * * 4478 0 0 P 11 * * * * * * * * * * * * 141 * * 3425 * * * * 11 0 * * * * * * 4620 0 0 P 12 4025 * * 3967 * 4419 * * 5513 4641 * * 2337 * 5484 953 * * * 5106 12 0 * * * * * * 4652 0 0 I 13 6464 * 6183 * 4811 * * 1249 * 3018 4595 * * * * * 6915 1620 * 5637 13 0 * * * * * * 5133 0 0 D 14 5015 * 1140 1585 * 6865 * * 4852 * * 3413 * * * 5686 * 5297 * * 14 0 * * * * * * 5208 0 0 E 15 4457 * 1546 2126 * * * 6595 3314 * * 4844 * 4149 5300 3320 5159 5600 * 7249 15 0 * * * * * * 5208 0 0 L 16 3922 2107 * * * * * 4556 * 730 5919 * * * * * 5263 6162 * * 16 0 * * * * * * 5208 0 0 L 17 6098 * * 6427 5581 * * 3468 6138 821 3035 * 6312 5593 6345 5296 4704 4297 * * 17 0 * * * * * * 5208 0 0 D 18 5461 * 2660 1721 * 6622 * * 2147 6577 6215 5872 6462 4618 5686 3082 4544 7304 * * 18 0 * * * * * * 5208 0 0 R 19 * * * 4313 * 6011 4530 4725 1229 4368 * 5120 5115 3449 3433 6258 6650 3541 * 5193 19 0 * * * * * * 5209 0 0 V 20 4098 6549 * * * 5142 * 1802 6062 5447 * 5305 * * * 5125 2909 1409 * 6112 20 65 4512 * 759 1289 * * 5215 1871 0 S 21 * * 1349 2989 * 3557 * * 4972 5866 * 3055 2633 4856 * 4994 * * * * 21 45 5011 * 2315 324 * * 5227 1749 0 S 22 * * 5277 * * * * * * * * 1472 * * * 763 5342 * * * 22 17 6407 * 0 * * * 5237 1000 0 K 23 * 6487 6328 * * * 6163 * 1478 * * * 4525 5021 1010 * 6979 * * 5347 23 0 * * * * * * 5282 0 0 Y 24 * * * * 1602 * * * * * * 5905 * 5646 * * * * * 658 24 0 * * * * * * 5282 0 0 A 25 2885 * 4533 3368 * 4623 * 4020 4272 3484 5882 5328 * 6809 3613 2348 3245 4912 * 6206 25 0 * * * * * * 5282 0 0 L 26 * * * * 5595 * * 3974 * 223 5414 * * * * 6345 * 6772 * 6165 26 0 * * * * * * 5281 0 0 V 27 3766 3703 * * * * * 3609 * * * * * * * 5119 3722 592 * * 27 0 * * * * * * 5281 0 0 I 28 4051 * * * * 6207 4083 2176 * 2546 3907 4549 * 5614 * 5199 3328 2198 * * 28 0 * * * * * * 5281 0 0 Y 29 2566 * * * 5143 * * 4263 * 1276 3822 * * * * * 5419 2160 * 5642 29 0 * * * * * * 5281 0 0 A 30 732 5298 * 6632 * 5968 * 4925 * * * * * * * 3342 4300 2608 * * 30 0 * * * * * * 5281 0 0 A 31 788 * * * * 5298 * 6596 5703 * * * * * * 2000 4010 4218 * * 31 0 * * * * * * 5281 0 0 K 32 6451 * * 4094 * * 6180 * 711 5585 6033 * * 3468 2631 * * 6683 * 7066 32 0 * * * * * * 5281 0 0 R 33 * * * * * * * * * * * * * 5852 78 * 6009 * * 5660 33 0 * * * * * * 5281 0 0 A 34 223 * * * * * * 5311 * * * * * * * 4888 5249 4112 * * 34 13 6807 * 4755 54 * * 5281 1000 0 R 35 * 5198 * * * * 3562 * 3672 5108 * 6033 * 4821 528 5907 * 6897 * 6437 35 15 * 6611 * * * * 5281 0 0 Q 36 7272 * 3697 2425 * 6149 * * 3925 5524 5536 6435 * 815 6624 * * 5891 * * 36 24 * 5943 * * * 0 5322 0 1000 I 37 * * * * * * 6037 1029 * 1226 6220 * * * 5042 * * * * 5408 37 80 6529 4528 0 * * 0 5303 1000 1560 N 38 2993 * 4688 5107 5706 6430 * 3065 6119 3874 5443 2152 * 4392 3218 4398 4293 3791 * * 38 90 * 4045 * * * 0 5224 0 2439 D 39 2798 * 2120 2148 * * * 5684 3614 * * 4864 * 4160 5126 3015 5755 5928 * 5516 39 562 * 1632 * * 2781 227 5228 0 2832 Y 40 * * 5963 2780 * 1945 6310 6049 3724 5320 3641 5015 * 4259 * 5913 4781 * * 2095 40 65 * 4495 * * * 0 5094 0 3892 Y 41 2278 * * 6107 4524 5556 * 4357 3929 3376 3979 5736 4778 3120 3545 3942 5570 5184 * 3818 41 141 * 3422 * * 4743 55 5082 0 3882 N 42 3506 5641 5668 2282 4373 * 4408 5157 3906 * 4528 2844 5187 3524 4453 3546 5131 * * 5662 42 193 4247 3781 2578 264 2852 215 4979 1672 4215 Q 43 3645 * 3828 2992 5163 4382 4548 * 5794 5879 * 4729 * 2127 5739 4541 2399 4899 * 5721 43 203 6232 3085 4000 93 2763 230 5009 1000 4151 L 44 4760 * * 2854 5739 3708 * * 3879 2009 * 3864 4421 3382 3285 3927 * 4901 * * 44 231 3943 3589 1998 416 751 1301 4904 1916 4391 Y 45 5950 * * 6427 * 693 3466 * * 6052 * 4143 * 4389 5960 5691 6072 4343 * 4501 45 17 6427 * 1000 1000 2530 274 5015 1000 3905 V 46 2671 * 2952 2800 * 4352 5000 4840 4777 3214 * * * * * 2775 6082 3456 * 4090 46 99 5156 4717 2634 253 2399 303 5100 1532 3697 G 47 4127 6729 7222 2658 * 2779 4832 5242 3248 4195 5626 6064 4400 5314 2818 3492 4880 6721 5697 * 47 141 5389 3854 2518 277 2197 355 5133 1402 3656 P 48 3975 * 4731 4892 * 5719 * * 5332 4743 * * 607 * * 5084 5433 3740 * * 48 96 5242 4721 2259 338 1465 649 5070 1610 3858 L 49 4619 * 5988 5679 5917 * * 6313 3134 1343 2980 * 5328 * 6239 5007 3044 4714 * 4988 49 91 * 4031 * * 2017 409 5061 0 3549 V 50 4676 * * 5061 * * * 2353 6365 2518 3523 6455 5045 4596 6046 * 5274 1568 * * 50 86 6113 4522 2585 263 1866 463 5112 1000 3808 E 51 4189 * 2594 2281 * 5408 * 6339 5617 3564 5961 5579 3742 4169 5766 3686 3730 3410 * * 51 38 * 5255 * * 1575 590 5048 0 3528 P 52 5567 * 3790 2771 6444 4789 3667 * 3403 * 6112 3557 3747 5837 3660 3961 2704 4959 6792 6662 52 15 * 6588 * * 1966 426 5112 0 3444 G 53 4428 5926 3936 2586 5195 3305 5904 * 3106 4763 * * 3897 5090 3481 5518 3648 4449 6614 3979 53 145 6081 3627 3585 126 1222 808 5137 1000 3217 L 54 5092 5768 3462 3276 5197 6403 5785 6663 2610 4403 5642 3886 4479 6547 3019 4897 4693 3489 * 4254 54 57 * 4699 * * 1033 968 5269 0 3271 Q 55 4557 5274 3231 4186 * 3264 * * 4186 6671 * 3035 * 5382 3830 1612 5334 4917 * * 55 83 5915 4670 1000 1000 734 1326 5189 1000 3064 E 56 5026 * 2184 2506 6488 6029 5308 * 2465 * 5697 2616 5308 6210 4857 5637 4894 5980 * 6036 56 65 4832 6834 2230 346 513 1741 5260 1807 2860 K 57 6588 * 5257 * * 5716 6253 * 286 * * 4249 * * 4098 * * * * * 57 63 5042 6321 1365 709 594 1566 5303 1627 1927 P 58 5912 * 4685 3889 4335 * * * * 5067 * 4064 817 * * 3843 5176 5889 * 4158 58 0 * * * * 0 * 5309 0 1431 L 59 * * * * * * 6031 3356 * 2271 * * 4238 * * 4914 2758 1165 * * 59 41 * 5152 * * * * 5320 0 0 S 60 * 6409 5184 5154 * 3000 * 6529 5282 * * 6186 * 6326 * 1888 2443 1782 * * 60 24 5941 * 2322 322 0 * 5320 1000 1799 I 61 5413 6102 * * * * * 1693 4283 3990 3317 5485 * 3721 3825 5409 3759 2673 6047 * 61 40 5185 * 1000 1000 * * 5320 1000 0 A 62 164 * * * * * * * * * * * * * * 3974 5944 5185 * * 62 0 * * * * * * 5320 0 0 L 63 6588 * * * 3745 * * 4186 * 678 3101 * * 6031 * * 5295 3685 * * 63 0 * * * * * * 5320 0 0 R 64 * * 5001 1630 * * 4292 5973 3164 5596 6578 4888 * 4334 1628 6946 6588 * 6562 * 64 0 * * * * * * 5320 0 0 E 65 * * * 60 * * * * * * * * * 5735 5527 * * * * * 65 0 * * * * * * 5320 0 0 I 66 * * * * 4486 * * 546 * 3097 4898 * * * * * * 3057 * * 66 0 * * * * * * 5320 0 0 H 67 1099 * 4289 4423 6984 4434 5224 4250 * 5185 5094 3768 * 6230 4765 5475 * 5252 7025 3937 67 0 * * * * * * 5320 0 0 A 68 1656 * 3354 2068 * 5071 6706 * 5578 * 6788 4922 * 4117 5000 3175 4495 * * * 68 0 * * * * * * 5253 0 0 D 69 * * 2861 5042 * 487 * * 4601 6032 * 5289 * * * 4775 * * * * 69 0 * * * * * * 5224 0 0 L 70 6043 * 5874 5162 5272 * 5488 6334 1024 2705 5383 6731 * 5836 4400 5989 3853 4554 * 6920 70 0 * * * * * * 5189 0 0 L 71 * * * * * * * 2023 * 1964 5302 * * * * * * 1082 * * 71 0 * * * * * * 5165 0 0 E 72 * * 2476 4249 * 3088 * * 3811 4983 * 4490 * * 5561 3122 1533 5561 * * 72 0 * * * * * * 4825 0 0 H 73 * 4602 * 5374 3987 * 3736 * 4083 * * * * 3921 4752 * * 3469 * 878 73 0 * * * * * * 4691 0 0 T 74 4424 * * 2108 * 2926 * * 4414 * * 4024 * 4144 * 2612 2799 3893 * 4312 74 0 * * * * * * 3946 0 0 E 75 * * 1871 2623 4445 * * * 4338 4115 * * * * * 2176 3719 4187 4082 * 75 0 * * * * * * 3873 0 0 G 76 * * * * * 0 * * * * * * * * * * * * * * 76 0 * * 0 * * * 2869 0 0 //