Align Probable 4-aminobutyrate aminotransferase; EC 2.6.1.19; (S)-3-amino-2-methylpropionate transaminase; EC 2.6.1.22; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT (uncharacterized)
to candidate WP_012471180.1 GLOV_RS15575 acetylornithine transaminase
Query= curated2:P94427 (436 letters) >NCBI__GCF_000020385.1:WP_012471180.1 Length = 399 Score = 249 bits (636), Expect = 1e-70 Identities = 149/432 (34%), Positives = 232/432 (53%), Gaps = 47/432 (10%) Query: 8 ITTAQWQQKRDQFVSKGVSNGNRSLAVKGEGAELYDLDGRRFIDFAGAIGTLNVGHSHPK 67 +T QW ++ D+ + K + V+GEG L+D DG+ ++DF + N+GH HPK Sbjct: 1 MTNQQWVERSDKVIMKTYGR-YPIVPVRGEGCRLWDADGKEYLDFLAGVAVNNLGHCHPK 59 Query: 68 VVEAVKRQAEELIHPGFNVMMYPTYIELAEKLCGIAPGSHEKKAIFLNSGAEAVENAVKI 127 VV+A++ QA LIH N P IELAE LC S KA F NSGAEA E A+K+ Sbjct: 60 VVKALQDQAATLIHCS-NYYQIPQQIELAELLCS---HSFADKAFFCNSGAEANEAAIKL 115 Query: 128 ARKYTK-------RQGVVSFTRGFHGRTNMTMSMTSKVKPYKFGFGPFAPEVYQAPFPYY 180 ARKY++ R G+++ FHGRT T+S T + K +F F P ++ Sbjct: 116 ARKYSREKHNNPERYGIITAADSFHGRTMATVSATGQEKVQRF----FDPLLH------- 164 Query: 181 YQKPAGMSDESYDDMVIQAFNDFFIASVAPETVACVVMEPVQGEGGFIIPSKRFVQHVAS 240 G + ++D+ + A+V P+T A +++EP+QGEGG IPS ++Q V Sbjct: 165 -----GFAHVPFNDLAALS------AAVTPQTCA-IMLEPIQGEGGINIPSMEYMQGVRE 212 Query: 241 FCKEHGIVFVADEIQTGFARTGTYFAIEHFDVVPDLITVSKSLAAGLPLSGVIGRAEMLD 300 C H ++ + DE+Q G RTG FA EHF + PD++T++K+LA G P+ ++ R E+ Sbjct: 213 LCDRHQLLLILDEVQVGMGRTGKLFAYEHFGITPDIMTLAKALAGGAPIGTMLARDEVAA 272 Query: 301 AAAPGELGGTYAGSPLGCAAALAVLDIIEEEGLNERSEEIGKIIEDKAYEWKQEFPFIGD 360 + PG G T+ G+PL AAA+A + I EEGL R+EE+G+ + + + F+ + Sbjct: 273 SFVPGTHGSTFGGNPLVTAAAVATVRAILEEGLLNRAEEMGEYLHGELERLGSRYSFVKE 332 Query: 361 IRRLGAMAAIEIVKDPDTREPDKTKAAAIAAYANQNGLLLLTAGINGNIIRFLTPLVISD 420 +R +G M + + I ++ G+LL + ++RF+ PL +S Sbjct: 333 VRGIGLMIGMSL----------SIPGGDIVKKGHEKGVLLNVT--HDTVLRFVPPLTVSK 380 Query: 421 SLLNEGLSILEA 432 +N + ILE+ Sbjct: 381 QEVNRMIEILES 392 Lambda K H 0.319 0.136 0.393 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: 424 Number of extensions: 25 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: 436 Length of database: 399 Length adjustment: 31 Effective length of query: 405 Effective length of database: 368 Effective search space: 149040 Effective search space used: 149040 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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