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 17422 b3359 bifunctional acetylornithine aminotransferase/ succinyldiaminopimelate aminotransferase (NCBI)
Query= SwissProt::P22256 (426 letters) >FitnessBrowser__Keio:17422 Length = 406 Score = 234 bits (598), Expect = 3e-66 Identities = 146/407 (35%), Positives = 218/407 (53%), Gaps = 42/407 (10%) Query: 22 IHPIFAD------RAENCRVWDVEGREYLDFAGGIAVLNTGHLHPKVVAAVEAQLKKLSH 75 I PI+A + + R+WD +G+EY+DFAGGIAV GH HP +V A++ Q + L H Sbjct: 17 ILPIYAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWH 76 Query: 76 TCFQVLAYEPYLELCEIMNQKVPGDFAKKTLLVTTGSEAVENAVKIAR--AATKRSG--- 130 V EP L L + + FA++ + + +G+EA E A K+AR A + S Sbjct: 77 IS-NVFTNEPALRLGRKL---IEATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKT 132 Query: 131 -TIAFSGAYHGRTHYTLALTGKVNPYSAGMGLMPGHVYRALYPCPLHGISEDDAIASIHR 189 IAF A+HGR+ +T+++ G+ YS G G P + P + + A+ H Sbjct: 133 KIIAFHNAFHGRSLFTVSVGGQPK-YSDGFGPKPADIIHV----PFNDLHAVKAVMDDHT 187 Query: 190 IFKNDAAPEDIAAIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEVQSGAGRTG 249 A+V+EP+QGEGG A++P F+Q LR LCD+H +L+ DEVQ G GRTG Sbjct: 188 -----------CAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTG 236 Query: 250 TLFAMEQMGVAPDLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAAL 309 LFA GV PD+ T AK++ GGFP++ + AE+ A PG G TY GNP+AC A Sbjct: 237 DLFAYMHYGVTPDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAG 296 Query: 310 EVLKVFEQENLLQKANDLGQKLKDGLLAIAEKHPEIGDVRGLGAMIAIELFEDGDHNKPD 369 + +L+ Q+ D L I +++ D+RG+G +I EL KP Sbjct: 297 AAFDIINTPEVLEGIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAEL-------KPQ 349 Query: 370 AKLTA-EIVARARDKGLILLSCGPYYNVLRILVPLTIEDAQIRQGLE 415 K A + + + G+++L+ GP +V+R L +EDA I +G++ Sbjct: 350 YKGRARDFLYAGAEAGVMVLNAGP--DVMRFAPSLVVEDADIDEGMQ 394 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: 474 Number of extensions: 20 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: 406 Length adjustment: 31 Effective length of query: 395 Effective length of database: 375 Effective search space: 148125 Effective search space used: 148125 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 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