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 WP_028740449.1 RL_RS02885 aspartate aminotransferase family protein
Query= SwissProt::P22256 (426 letters) >NCBI__GCF_000009265.1:WP_028740449.1 Length = 399 Score = 210 bits (534), Expect = 7e-59 Identities = 140/412 (33%), Positives = 205/412 (49%), Gaps = 45/412 (10%) Query: 24 PIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSH--TCFQVL 81 P+ +R E + G YLDF G+AV + GH +P VV A++ Q K+ H +++ Sbjct: 15 PLRFERGEGVWLITESGERYLDFGAGVAVTSVGHSNPHVVGALKEQADKVWHLSNIYEIP 74 Query: 82 AYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIAR------AATKRSGTIAFS 135 E + + FA K +G+EA+E A+K AR +R I F Sbjct: 75 GQE------RLAKRLTDATFADKVFFTNSGAEALECAIKTARRYQFSKGHPERFHIITFE 128 Query: 136 GAYHGRTHYTLALTGKVNPYSAGMG-LMPGHVYRALYPCPLHGISEDDAIASIHRIFKND 194 GA+HGRT T+A G+ Y G G PG + A I + Sbjct: 129 GAFHGRTLATIAAGGQ-EKYLEGFGPKAPGF--------------DQVAFGDIEAV--RA 171 Query: 195 AAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGTLFAM 254 A E AAI+IEPVQGEGG ++P FM+ LR LCD++G++LI DEVQ+G GRTG LFA Sbjct: 172 AITEATAAILIEPVQGEGGVRPATPEFMKALRQLCDDNGLLLILDEVQTGVGRTGKLFAH 231 Query: 255 EQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKV 314 E G+ PD+ AK I GGFPL AE + G G TY GNP+A VL + Sbjct: 232 EWSGITPDIMAVAKGIGGGFPLGACLATAEAASGMKAGTHGSTYGGNPLAMAVGSAVLDI 291 Query: 315 FEQENLLQKANDLGQKLKDGLLAIAEKHPE-IGDVRGLGAMIAIELFEDGDHNKPDAKLT 373 + LQ+ D+ + GL ++ +++P+ I D+RG G ++ I+ A + Sbjct: 292 ILADGFLQQVRDVALVFRQGLASLKDRYPDVIEDIRGEGLLLGIKA----------AVPS 341 Query: 374 AEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQCFDEAK 425 AE++ R L+ + G NV+R+L PL + + R+GL I + + + Sbjct: 342 AELLQAIRAAHLLGVPAGD--NVIRLLPPLVVTAEEAREGLVRIERAAESIR 391 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: 438 Number of extensions: 24 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: 399 Length adjustment: 31 Effective length of query: 395 Effective length of database: 368 Effective search space: 145360 Effective search space used: 145360 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: 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