Align branched-chain-amino-acid transaminase (EC 2.6.1.42); glutamate-prephenate aminotransferase (EC 2.6.1.79) (characterized)
to candidate WP_015411527.1 MM_RS05445 branched-chain-amino-acid transaminase
Query= BRENDA::P54691 (305 letters) >NCBI__GCF_000007065.1:WP_015411527.1 Length = 292 Score = 131 bits (329), Expect = 2e-35 Identities = 98/297 (32%), Positives = 155/297 (52%), Gaps = 30/297 (10%) Query: 7 IAYFEDKFVPFEDAKISVATHALHYGTAAFGGLRGIPDPEDPGTILLFRLDRHGDRLSKS 66 + Y + KFVP +AK+SV H YG F G+R +F+L H DRL S Sbjct: 5 LIYLDGKFVPKSEAKVSVYDHGYLYGDGVFEGIRAYNGR-------VFKLKEHVDRLFDS 57 Query: 67 AKFLHYDI--SAEKIKEVIVDFVKKNQPDKSFYIRPLVYSS--GLGIAPRLHNLEKDFLV 122 AK + DI + E++ E+I++ ++KN K YIRP+V LG+ PR EK +V Sbjct: 58 AKAIAMDIPVTREEMTEIILETLRKNNL-KDAYIRPIVSRGVGDLGLDPR--KCEKPCVV 114 Query: 123 -----YGLEMGDY--LAADGVSCRISSWYRQEDRSFPLRGKI-SAAYITSALAKTEAVES 174 +G G+ + GVS + + + L I S Y+ + LAK EA E Sbjct: 115 VIAQGWGAMYGNLYEIGLTGVSVCV-----RRNAPDALSPNIKSLNYLNNILAKIEANEK 169 Query: 175 GFDEAILMNSQGKVCEATGMNVFMVRNGQIVTPGNEQDILEGITRDSILTIAADLGIPTC 234 G DEAI ++ G VCE +G N+F+V+N ++ TP + L+GITR + + + ++G Sbjct: 170 GGDEAIFLDQNGFVCEGSGDNIFIVKNDKVFTPHTISN-LKGITRATAIELLDEMGYKVI 228 Query: 235 QRPIDKSELMIADEVFLSGTAAKITPVKRIENFTLGGDR--PITEKLRSVLTAVTEN 289 + + +L ADE+F++GTAA+ PV R++ +G + P+T K+ +T + Sbjct: 229 EANLGLFDLYTADEIFVTGTAAESAPVTRLDGRIIGNGKPGPLTMKMVEAFDKITRS 285 Lambda K H 0.320 0.138 0.406 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: 242 Number of extensions: 18 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: 305 Length of database: 292 Length adjustment: 27 Effective length of query: 278 Effective length of database: 265 Effective search space: 73670 Effective search space used: 73670 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: 48 (23.1 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