Align 4-aminobutyrate aminotransferase GabT; (S)-3-amino-2-methylpropionate transaminase; GABA aminotransferase; GABA-AT; Gamma-amino-N-butyrate transaminase; GABA transaminase; Glutamate:succinic semialdehyde transaminase; L-AIBAT; EC 2.6.1.19; EC 2.6.1.22 (characterized)
to candidate HSERO_RS19685 HSERO_RS19685 4-aminobutyrate aminotransferase
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__HerbieS:HSERO_RS19685 Length = 456 Score = 228 bits (580), Expect = 4e-64 Identities = 147/425 (34%), Positives = 230/425 (54%), Gaps = 25/425 (5%) Query: 8 MQRRSQAIPRGVGQIHPIFADRAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVE 67 + R++++ RG G++ PI D+A D +G ++D + G+ V + G +P+VV A+ Sbjct: 33 LSARTESMARGGGRM-PIAMDQAFGVTFKDPDGNTFIDLSAGVGVSSVGRCNPRVVEAIR 91 Query: 68 AQLKKLSHTCFQVLAYEPYL--ELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIARAA 125 Q + L H+ + L ++ EIM + GD T GS+A+E AVK A+ Sbjct: 92 KQSESLMHSMEVNSSKRTELAAKISEIMPDGLRGDCI--TFFTQGGSDALEAAVKFAKRV 149 Query: 126 TKRSGTIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPL-------HGI 178 T R IAF G YHG + + ALT Y G G G V A YP H Sbjct: 150 TGRHQIIAFHGGYHGIWNASNALTTGT-AYRKGFGPFMGGVIHAPYPYAYRFPFDTSHKS 208 Query: 179 SEDDAIASIHRIFKND-AAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLI 237 +E A + + A +D+AA+++EPVQGEGG+ SP F+Q LR CD G +LI Sbjct: 209 AEQIAGEYVDYLLNTPYTAADDVAAVIVEPVQGEGGYVPPSPEFLQILRKACDRSGALLI 268 Query: 238 ADEVQSGAGRTGTLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGT 297 DEVQ+GAGRTG ++A+E GV PD+ TF K I G P+AG+ R+++ + G T Sbjct: 269 VDEVQAGAGRTGKMWAVEHSGVKPDMLTFGKGIGGDMPMAGLVMRSDLAAKIPDGSQPNT 328 Query: 298 YAGNPIACVAALEVLKVFEQE--NLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMI 355 +A N I+ AL + + + +L+ +A+ LG + ++ + + P +G+VRG G MI Sbjct: 329 FAANSISAAVALTNISILQDPRLDLVNRAHTLGLEAQERIRSF--NSPWVGEVRGRGLMI 386 Query: 356 AIELFEDGDHNKPDAKLTAEIVARARD----KGLILLSCGPYYNVLRILVPLTIEDAQIR 411 IEL E+ + +P L+ E + + D G++++ CG Y NV+R++ LTI + + Sbjct: 387 GIELVENRETREP---LSREKLGKLMDYVVGHGVLMIPCGRYTNVMRVMPSLTIPRSLMF 443 Query: 412 QGLEI 416 +GL+I Sbjct: 444 KGLDI 448 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: 525 Number of extensions: 31 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: 456 Length adjustment: 32 Effective length of query: 394 Effective length of database: 424 Effective search space: 167056 Effective search space used: 167056 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 Aug 03 2021. The underlying query database was built on Aug 03 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