Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_010531796.1 ON01_RS14505 sulfoacetaldehyde acetyltransferase
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000224785.1:WP_010531796.1 Length = 590 Score = 243 bits (620), Expect = 2e-68 Identities = 176/554 (31%), Positives = 277/554 (50%), Gaps = 17/554 (3%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 +M +E +V L E ++ V+G G A + + D L I VRHEQ+A H AD Y Sbjct: 17 KMTPSEAIVETLVAENIKEVYGIVGSAFMDMLD-LFPAAGIRFIPVRHEQSAGHMADAYE 75 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 R +G GV + +GPG+TN VT +A A P+VVI+ + T+AIG D FQE + V I Sbjct: 76 RVSGTAGVIVGQNGPGITNMVTSVAAANQAHSPLVVISPSAGTNAIGMDGFQEANQVSIF 135 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 + I K V + +A ++ AF IA R GPV+ DIP+D+ + + R+ Sbjct: 136 KDITKETVQVTNKNRVADKLRTAFRIAYAER-GPVLFDIPRDLFYGEVEDVILEPHQYRA 194 Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLMGL 257 + G I AV LL+ A+ P I +G G V A D + ++A P M Sbjct: 195 -DKRGVGDPASIEHAVELLKNAKNPAIISGRGSVDAEGVDSVVKIAEYLTAPGATAYMHN 253 Query: 258 GAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGAR---FDDRVIGNPAHFTSQARKI 314 AFP VG +G G A ++Q DV++A+G R F + +F + A KI Sbjct: 254 DAFPADHPLAVGPIGYMGAKSAMYSLQEADVVLAVGTRLSQFGTLPCYDIDYFPTHA-KI 312 Query: 315 IHIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKR-----EALAKWWEQIE 369 I IDI+P I + V++ I+G+ K E+ Q+K + P++ +A+ K E+ E Sbjct: 313 IQIDINPRQIGRTHPVEVGIIGDAKAASDEIYRQLKLAMPSPEKDNERIQAVTKRKEEWE 372 Query: 370 QWRSVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKFDEPRRWI 429 Q VD D + I P+ + ++ +A + SD+G A + KF++ RR I Sbjct: 373 Q-ELVDSAMED--GDPINPRRALLEMTRAMPENAIVSSDIGNVSSTANAYLKFNQTRRHI 429 Query: 430 NSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNN 489 + G G P A+G + A P+ V I G+G+ M + E+ST ++ + PV C NN Sbjct: 430 AALTFGNTGFAYPAALGAQLAEPDAPVFAIVGDGAWGMSLHEVSTAVEQNIPVIACVFNN 489 Query: 490 GYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLK 549 ++ Q YD+RY S + A P+F ++A++ G +G ++K D+ PA+ + + + Sbjct: 490 KAWAAEKKNQVDYYDDRYVGSDIKA-PEFAEVAKSMGALGYTIDKPEDIGPAIEDVLKQR 548 Query: 550 DRTVFLDFQTDPTE 563 V L+ D T+ Sbjct: 549 KPAV-LNIYVDGTQ 561 Lambda K H 0.319 0.135 0.407 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 772 Number of extensions: 43 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 585 Length of database: 590 Length adjustment: 37 Effective length of query: 548 Effective length of database: 553 Effective search space: 303044 Effective search space used: 303044 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory