Align 4-aminobutyrate aminotransferase GabT; 5-aminovalerate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.48 (characterized)
to candidate 3608039 Dshi_1446 aminotransferase class-III (RefSeq)
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__Dino:3608039 Length = 444 Score = 198 bits (504), Expect = 2e-55 Identities = 140/420 (33%), Positives = 206/420 (49%), Gaps = 31/420 (7%) Query: 33 CRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSHTCFQVLAYEPYLELCEI 92 C + D +G+ YLD +GG AV GH HP V AA+ AQ+ K++ EP LC+ Sbjct: 22 CYIIDADGKRYLDGSGGAAVSCLGHDHPAVRAALHAQIDKIAFAHTGFFTSEPAEVLCDA 81 Query: 93 MNQKVPGDFAKKTLLVTTGSEAVENAVKIAR------AATKRSGTIAFSGAYHGRTHYTL 146 + P +K L++ GSE+VE A+K+AR +R IA +YHG T L Sbjct: 82 LIAAAPKGI-EKVYLLSGGSESVEAALKLARQFFLETGEPRRHRVIARRQSYHGNTLGAL 140 Query: 147 ALTGKVNPYSAGMGLMPGHVYRALYPCPLH---GISEDDAI-----ASIHRIFKNDAAPE 198 A G L+ + + PC + + E DA A R PE Sbjct: 141 AAGGNAWRREKYAPLLVETYH--IDPCYAYRHQAVGESDAAYGRRAADALRTEIERLGPE 198 Query: 199 DIAAIVIEPVQGE-GGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAMEQM 257 + A + EPV G G +P + +R+R +CDE+G++LI DEV G GRTGTLFA EQ Sbjct: 199 TVMAFIAEPVVGATAGAVPPAPGYFERIREICDEYGVLLILDEVMCGMGRTGTLFACEQD 258 Query: 258 GVAPDLTTFAKSIAGGF-PLAGVTGRAEVMDAVAPGG----LGGTYAGNPIACVAALEVL 312 G++PD+ T AK + G+ P+ + + DA+A G G TY G+P+A AA V+ Sbjct: 259 GISPDIVTIAKGLGAGYAPIGAMLASGRIYDAIAQGSGSFQHGHTYHGHPLAAAAAGAVV 318 Query: 313 KVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNK---PD 369 + + + G L+ L A +H +GD+RG G IEL ED D + P Sbjct: 319 ETLRAPGTMAQVRAKGATLQSRLEAALGQHSHVGDIRGRGLFRGIELVEDRDTKRPLDPA 378 Query: 370 AKLTAEIVARARDKGLILLS-----CGPYYNVLRILVPLTIEDAQIRQGLEIISQCFDEA 424 K++A I A A +GLI G + + + + P IED QI + ++++ D+A Sbjct: 379 RKVSARIKAAAMARGLICYPGSGTIDGKHGDHILLAPPFIIEDKQIDALVHMLAEAIDDA 438 Lambda K H 0.320 0.137 0.401 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: 530 Number of extensions: 33 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: 426 Length of database: 444 Length adjustment: 32 Effective length of query: 394 Effective length of database: 412 Effective search space: 162328 Effective search space used: 162328 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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