Align Acetolactate synthase large subunit; AHAS; EC 2.2.1.6; Acetohydroxy-acid synthase large subunit; ALS (uncharacterized)
to candidate WP_012468868.1 GLOV_RS03855 thiamine pyrophosphate-binding protein
Query= curated2:Q02137 (575 letters) >NCBI__GCF_000020385.1:WP_012468868.1 Length = 598 Score = 242 bits (617), Expect = 4e-68 Identities = 177/579 (30%), Positives = 285/579 (49%), Gaps = 45/579 (7%) Query: 13 SQLVLQTLKELGVEIIFGYPGGAMLPLYDAIHNFEGIQHILARHEQGATHEAEGYAKSSG 72 S + + E G+ +F GG + L D++ N + HEQ AE YA+ +G Sbjct: 6 SDYIASFMVENGITDLFTVTGGGAMHLNDSLGNHPELVSTYNHHEQACAIAAEAYARLTG 65 Query: 73 KVGVVVVTSGPGATNAVTGIADAYLDSVPLLVFTGQVG----------PL-SIGKDAFQE 121 ++ +V VTSGPG TNA+TG+ ++DS+P+ V +GQV PL +G F Sbjct: 66 RIALVCVTSGPGGTNAITGVMGGWVDSIPMFVISGQVKFSTTIASTNVPLRQLGDQEFNI 125 Query: 122 ADTVGITAPITKYNYQIRETADIPRIVTEAYYLARTGRPGPVEIDLPKDV-STLEVTEIN 180 D+V +TKY + E I + A +LA GRPGPV +D+P +V L T+ Sbjct: 126 VDSVRC---MTKYAVMLTEPESIAYHLERALFLAGHGRPGPVWLDIPLNVQGALIETDA- 181 Query: 181 DPSLNLPHYHESEKA-------TDEQLQELLTELSVSKKPVIIAGGGINYSGSVDIFRAF 233 L HY SE A +++ +L+ ++ ++KPVI+AG GI SGS D+F Sbjct: 182 -----LQHYDPSEDAVQVVAPPSNDVYSQLIEKICNARKPVILAGSGIRLSGSHDVFIQL 236 Query: 234 VEKYQIPVVSTLLGLGTLPISHELQLGMAGMHGSYAANMALVEADYIINLGSRFDDRVVS 293 +EK IPVV+ L H L G G G+ N + D +++LG R + R +S Sbjct: 237 LEKLNIPVVTAWNAHDNLWDDHPLYCGRPGTIGTRGGNFVVQNCDLLLSLGCRMNIRQIS 296 Query: 294 -NPAKVAKNAVVAHIDIDAAELGKIVKT-DIPILSDLKAALSRLLQLNKVRTDFN----D 347 N AK+A + +DIDA EL K T D+PI +DL L L L ++ D + Sbjct: 297 YNWENFAKDAYLVAVDIDAGELKKPTLTVDMPIHADLGDFLPGL--LGAMQADHKLGNIE 354 Query: 348 WIKTVTKNKEK----APFTYEPQNHDIRPQETIKLIGEYTQGDAIIVTDVGQHQMWVAQY 403 W++ K +K P Y P + + P + + +Y + VT G + Q Sbjct: 355 WLEWCRKINQKYPAVQPHHYTPHS-PVNPYVFMDRLSQYLDEGDVTVTGNGSACVCSFQA 413 Query: 404 YPYKNARQLITSGGMGTMGFGIPAAIGAKLAQPNKNVIVFVGDGGFQMTNQELALLNGYG 463 K ++L T+ G +MG+G+PAA+GA +A K VI GDG QM QEL + Sbjct: 414 MVIKKNQRLFTNSGCASMGYGLPAALGAAVALGGKRVICLDGDGSIQMNLQELQTIIHNK 473 Query: 464 IAIKVVLINNHSLGMVRQWQESFYEER---RSQSVFDVEPNFQLLAEAYGIKHVKLDNPK 520 + +K+ +NN +RQ Q + + R +++ P+ +A AYG + +K+D + Sbjct: 474 LNLKIFWLNNDGYHSIRQTQTNIFNARFCGVNETSGISFPSADKIARAYGFEFIKIDAVE 533 Query: 521 TLADDL-KIITEDEPMLIEVLISKSEHVLPMIPAGLHSD 558 + + + K++ D ++ EV+++ ++ P + + + D Sbjct: 534 DMDEKIKKVLLSDTSIVCEVILNPAQGFEPKLSSRILQD 572 Lambda K H 0.316 0.135 0.385 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: 811 Number of extensions: 38 Number of successful extensions: 5 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: 575 Length of database: 598 Length adjustment: 37 Effective length of query: 538 Effective length of database: 561 Effective search space: 301818 Effective search space used: 301818 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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