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 PfGW456L13_4982 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4982 Length = 416 Score = 348 bits (893), Expect = e-100 Identities = 182/419 (43%), Positives = 258/419 (61%), Gaps = 18/419 (4%) Query: 11 RSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQL 70 RS+ I + + +HP+ +N VWD +G+ Y+DF GGI VLN GH HP++V A+ Q Sbjct: 2 RSETISQSINIVHPVTLSHGKNAEVWDTDGKRYIDFVGGIGVLNLGHCHPRIVEAIREQA 61 Query: 71 KKLSHTCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAATKRSG 130 +L+H F +EPYLEL + ++ +P + +L +G+EA ENA+KI R AT RS Sbjct: 62 TRLTHYAFNAAPHEPYLELMDCLSAFMPVGYPVSGMLTNSGAEAAENALKIVRGATGRSA 121 Query: 131 TIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHRI 190 IAF GA+HGRT TL L GKV PY +G++PG V+ +P +G++ +A+ ++ R+ Sbjct: 122 VIAFDGAFHGRTLATLNLNGKVAPYKQKVGVLPGPVFHLPFPSRDNGVTCAEALKAMERL 181 Query: 191 FKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTGT 250 F + ED+A ++EPVQGE GF A F Q LR CD+ GI+LIADE+QSG GRTG Sbjct: 182 FSVEIDVEDVACFIVEPVQGEAGFLAMDIEFAQALRKFCDDKGIVLIADEIQSGFGRTGE 241 Query: 251 LFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALE 310 FA ++G+ PDL KSIAGG PL V GR ++D + GGLGGTY+GNPIAC AAL Sbjct: 242 RFAFSRLGIEPDLILLGKSIAGGVPLGAVVGRKSLLDNLPKGGLGGTYSGNPIACAAALA 301 Query: 311 VLKVFEQENLLQKANDLGQKLKDGLLAIAEKH---------PEIGDVRGLGAMIAIELFE 361 L NL + G + ++ AI +H P +G + G+GAM IEL Sbjct: 302 TLDEMNDANL----HAWGTQQEE---AIVGRHATWRANNLTPYLGRLTGVGAMRGIELI- 353 Query: 362 DGDHNKPDAKLTAEIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLEIISQC 420 + D + A+LT +++A ARD GL+L+ G +++R+L PLTIE A + +GL+I+ C Sbjct: 354 NADGSPAAAQLT-QLLALARDAGLLLMPSGKSRHIIRLLAPLTIEAAVLEEGLDILEAC 411 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: 492 Number of extensions: 13 Number of successful extensions: 3 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: 416 Length adjustment: 32 Effective length of query: 394 Effective length of database: 384 Effective search space: 151296 Effective search space used: 151296 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 Apr 09 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