Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate WP_015945362.1 DHAF_RS23135 sulfoacetaldehyde acetyltransferase
Query= metacyc::MONOMER-18810 (585 letters) >NCBI__GCF_000021925.1:WP_015945362.1 Length = 581 Score = 231 bits (590), Expect = 5e-65 Identities = 177/561 (31%), Positives = 268/561 (47%), Gaps = 30/561 (5%) Query: 18 EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77 +M +E + L EG+ +V G G A + + D L E I VRHEQ+A H D + Sbjct: 5 KMTPSEAICETLVAEGITHVSGIVGSAFMDLID-LFPTAGIEFISVRHEQSAGHMEDAFC 63 Query: 78 RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137 R TGK GV + +GPG+TN VT +A A PMV+I + T +G D FQE DTV I Sbjct: 64 RVTGKAGVIIGQNGPGITNMVTSVAAANSAHTPMVIICPSAGTPTVGWDGFQEADTVQIF 123 Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197 + I K V A ++ AF IA R GPV+ DIP+D + + ++ Sbjct: 124 KAITKAAIQVPHPSRAADCLRTAFRIAYAER-GPVLYDIPRDYFYGEVEEQI---LEPHQ 179 Query: 198 YNPVNK--GHSGQIRKAVALLQGAERPYIYTGGGVVLANASDELRQLAALTGHPVTNTLM 255 Y + G + KA LL AERP I +G GVV A D + +A L PV T + Sbjct: 180 YRVSQRGCGDLASLDKAAELLFSAERPVIISGRGVVDTQARDIVAGIAGLLTAPVACTYL 239 Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGN----PAHFTSQA 311 AFP +VG +G G+ A ++ DV++A+G R V G ++ + Sbjct: 240 HNDAFPADHPLWVGPIGYMGSKAAMHSLAEADVILALGTRLS--VFGTLPQYDINYFPEN 297 Query: 312 RKIIHIDIDPSSISKRVKVDIPIVGN----VKDVLQELIAQIKASDIKPKREALAK---- 363 KII +DI+P I++ V+I I+ + K++L+ L A+I A ++ R A K Sbjct: 298 AKIIQVDINPRHIARTHPVEIGIIADAKEAAKEILKRLEAKIPAPEVNKGRLATIKARQK 357 Query: 364 -WWEQIEQWRSVDCLKYDRSSEIIKPQYVVEKIWELTKGDAFICSDVGQHQMWAAQFYKF 422 W ++I VD + I P+ + ++ + +A + +D+G A + KF Sbjct: 358 DWEDEIVSLAMVD-------GDPINPRRGLYEVQKALPENAIVATDIGNVSSTANSYLKF 410 Query: 423 DEPRRWINSGGLGTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPV 482 I + G G P A+G + A VV I G+G+ M + E+ST ++ + PV Sbjct: 411 TGKGMHIAALTFGNTGFAYPAALGAQLADRNAPVVAIIGDGAWGMSLHEVSTAVEQNLPV 470 Query: 483 KICSLNNGYLGMVRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPAL 542 NG ++ Q Y+NR+ + + FV +A A G G+R+EK +V PAL Sbjct: 471 VAIVFRNGGWCAEKKNQVDFYNNRFVGADIPNPESFVPVAIAMGAEGVRIEKAEEVGPAL 530 Query: 543 REAFRLKDRTVFLDFQTDPTE 563 A + TV L+ D T+ Sbjct: 531 ARALAARKPTV-LEIVCDGTQ 550 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: 754 Number of extensions: 36 Number of successful extensions: 4 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: 581 Length adjustment: 36 Effective length of query: 549 Effective length of database: 545 Effective search space: 299205 Effective search space used: 299205 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 Apr 10 2024. The underlying query database was built on Apr 09 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