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 N515DRAFT_3630 N515DRAFT_3630 4-aminobutyrate aminotransferase
Query= curated2:P94427 (436 letters) >FitnessBrowser__Dyella79:N515DRAFT_3630 Length = 469 Score = 179 bits (455), Expect = 1e-49 Identities = 130/421 (30%), Positives = 206/421 (48%), Gaps = 30/421 (7%) Query: 36 GEGAELYDLDGRRFIDFAGAIGTLNVGHSHPKVVEAVKRQAEELIHPGFNVMMYPTYIEL 95 G+G+ +YD G F+D +N G+ + ++ + +K Q + L + ++ T IEL Sbjct: 44 GQGSWMYDTAGVPFLDLQMWYSAVNFGYGNKRLNDTLKAQIDTLPQVA-SQYLHQTRIEL 102 Query: 96 AEKLCGIAPGSHEKKAI-----FLNSGAEAVENAVKIARKYTKRQGVV-SFTRGFHGRTN 149 A+ IA + +K + F GA+AVE+++K+ R Y + ++ +F G+HGRT Sbjct: 103 AKT---IAVDAQQKFGLKGRVHFNVGGAQAVEDSLKLVRNYKNGKSLMFAFEGGYHGRTL 159 Query: 150 MTMSMTSKVKPYKFGFGPFAPEVYQAPFPYYYQKPAGMSDESYDDMVIQAFNDFFIAS-- 207 S+TS + Y+ FG F PFPY +++P GM+ E Y D ++ F F Sbjct: 160 GASSITSSYR-YRRRFGHFGERAMFIPFPYPFRRPKGMTPEEYSDACVRQFERLFETEYN 218 Query: 208 ------VAPETVACVVMEPVQGEGGFIIPSKRFVQHVASFCKEHGIVFVADEIQTGFART 261 V A +EP+QG GG++IP K F + + ++GI+ V DEIQ GF RT Sbjct: 219 GVWDPKVNQAEYAAFYVEPIQGTGGYVIPPKNFFKDLKKVLDKYGILMVVDEIQMGFWRT 278 Query: 262 GTYFAIEHFDVVPDLITVSKSLAAGL-PLSGVIGRAEML--DAAAPGELGGTYAGSPLGC 318 G ++IEHF V PD+I K+L GL PLSG+ R EM+ + PG T+ +PLG Sbjct: 279 GKLWSIEHFGVTPDIIVFGKALTNGLNPLSGLWAREEMINPEIFPPGSTHSTFNSNPLGT 338 Query: 319 AAALAVLDIIEEEGLNERSEEIGKIIEDKAYEWKQEFPFIGDIRRLGAMAAIEIVKD--- 375 + L V+ + E + G D + ++ IGD+ LG EI D Sbjct: 339 SLGLEVIKMGYELDYETNVAKKGAHFLDALKDLQKRHKEIGDVDGLGLALRAEICTDDGF 398 Query: 376 -PDTREPDKTKAAAIAAYANQN----GLLLLTAGINGNIIRFLTPLVISDSLLNEGLSIL 430 P+ D+ +A N GL+L G N+I F L I+ ++ +++L Sbjct: 399 TPNKALLDRMVDIGLAGDLEHNGKKIGLVLDVGGWYKNVITFAPSLDITHEEIDLAIALL 458 Query: 431 E 431 + Sbjct: 459 D 459 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: 468 Number of extensions: 32 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: 436 Length of database: 469 Length adjustment: 33 Effective length of query: 403 Effective length of database: 436 Effective search space: 175708 Effective search space used: 175708 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: 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