Align acetolactate synthase (EC 2.2.1.6) (characterized)
to candidate WP_028315016.1 G491_RS0113880 thiamine pyrophosphate-binding protein
Query= BRENDA::P9WG39 (547 letters) >NCBI__GCF_000429905.1:WP_028315016.1 Length = 555 Score = 288 bits (736), Expect = 5e-82 Identities = 190/541 (35%), Positives = 279/541 (51%), Gaps = 17/541 (3%) Query: 14 GRLIARRLKA-SGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAAFAAEGWSKVTR 72 G L+A+ LK G++ VFTLSG H+ +I DG E GIR +D RHEQ A+ A WS T Sbjct: 7 GHLVAKYLKEIEGVEAVFTLSGAHIENILDGLNEFGIRSVDVRHEQAASMMAHAWSLYTG 66 Query: 73 VPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGGRAPALRWGMGSLQEIDHVPFVAPVA 132 PGV +TAGPG TN ++ +A A + +PLVVL GR P G+LQE++ + V V Sbjct: 67 KPGVCLVTAGPGFTNALTGIANAFLDNAPLVVLCGRHPLRDDLKGALQEMNQIDMVKSVV 126 Query: 133 RFAATAQSAENAGLLVDQALQAAVSAPSGVAFVDFPMDHAFSMSSDNGR---PGALTELP 189 +++AT + + A + AV G F++ P D S++ D P T L Sbjct: 127 KWSATCHDIKRIPEYLSIAFRQAVEGRPGPVFLELPPD-ILSIAVDLKSVDIPKRRT-LK 184 Query: 190 AGPTPAGDALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLVEERHIPVLMNGMARGV 249 TP + L AA L+ A+RP+++ G+ V + + E+ IP + RG Sbjct: 185 TSVTPVKEDLKAAAKLIDQAKRPLLIGGSGVGFSECGKQVAAFAEKTGIPFALLNNGRGA 244 Query: 250 VPADHRLAFS----RARSKALGEADVALIVGVPMDFRLGFGGVFGSTTQLIVADRVEPAR 305 +P H + + A AL + D+ +IVG+ +++ + G F +V ++P Sbjct: 245 LPDSHPRSINDGGFTAVMAALPQVDLVIIVGLRLNWVMESGQTFPDAK--VVRIDIDPTE 302 Query: 306 -EHPRPVAAGLYGDLTATLSALAGS-GGTDHQGWIEELATAETMARDLEKAELVDDRIPL 363 + R GL GD L L D W ++L A E+ + P+ Sbjct: 303 IDRNRTSDVGLAGDAGQILDLLTPMVASKDRSQWEKDLRAAYGAFLVTEREQRETPSYPI 362 Query: 364 HPMRVYAELAALLERDALVVIDAGDFGSYAGRMIDS-YLPGCWLD-SGPFGCLGSGPGYA 421 HP R+ A++ ++ DA V+D GD Y S + G S GC+G+G +A Sbjct: 363 HPNRLVAQIQKVVGEDAYYVVDGGDTSYYGSAGFSSIHKAGVTAPASSLLGCIGTGVPFA 422 Query: 422 LAAKLARPQRQVVLLQGDGAFGFSGMEWDTLVRHNVAVVSVIGNNGIWGLEKHPMEALYG 481 LAAK+A P + V+LL GDG+FGF+GME+DT VR N+ +V V+ N+ WG+ KH E G Sbjct: 423 LAAKIAHPNKPVILLNGDGSFGFNGMEFDTAVRLNIPIVCVVNNDCAWGMIKHAQEMSIG 482 Query: 482 YSVVAELRPGTR-YDEVVRALGGHGELVSVPAELRPALERAFASGLPAVVNVLTDPSVAY 540 GTR Y+++V ALGG+GE V ++ PAL+RA SG PA VNV+TD + Sbjct: 483 PERCTCSELGTRHYEKMVEALGGYGEFVEKDEDIVPALKRAIESGKPACVNVMTDCTAVS 542 Query: 541 P 541 P Sbjct: 543 P 543 Score = 26.9 bits (58), Expect = 0.002 Identities = 23/101 (22%), Positives = 40/101 (39%), Gaps = 19/101 (18%) Query: 7 PAQTMHAGRLIARRLKASGIDTVFTLSGGHLFSIYDGCREEGIRLIDTRHEQTAAFAAEG 66 P+ +H RL+A+ K G D + + GG DT + +A F++ Sbjct: 358 PSYPIHPNRLVAQIQKVVGEDAYYVVDGG-----------------DTSYYGSAGFSSIH 400 Query: 67 WSKVTRVPGVAALTAGPGITNGMSAMAAAQQNQSPLVVLGG 107 + VT G G+ ++A A P+++L G Sbjct: 401 KAGVTAPASSLLGCIGTGVPFALAAKIA--HPNKPVILLNG 439 Lambda K H 0.319 0.135 0.405 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: 694 Number of extensions: 31 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 547 Length of database: 555 Length adjustment: 36 Effective length of query: 511 Effective length of database: 519 Effective search space: 265209 Effective search space used: 265209 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