Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate BWI76_RS26000 BWI76_RS26000 aspartate aminotransferase family protein
Query= metacyc::MONOMER-11537 (425 letters) >FitnessBrowser__Koxy:BWI76_RS26000 Length = 406 Score = 224 bits (571), Expect = 4e-63 Identities = 146/409 (35%), Positives = 217/409 (53%), Gaps = 46/409 (11%) Query: 23 IHPIFADS------AKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTH 76 I PI+A + K + V D +G+E++DFAGGIAV GH HP ++AA+ EQ KL H Sbjct: 17 ILPIYAPAEFIPVKGKGSRVWDQQGKEYVDFAGGIAVTALGHCHPALVAALHEQGEKLWH 76 Query: 77 TCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARAATG------RA 130 T V EP + L K+ V FA + + + +G+EA E A K+AR T + Sbjct: 77 TS-NVFTNEPALRLGRKL---VDATFADRVVFMNSGTEANETAFKLARHYTVTRHSPYKT 132 Query: 131 GVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS--IDDSIASI 188 +IAF A+HGR++ T+ + G+ YS G G P I + N+LH V +DD Sbjct: 133 KIIAFHNAFHGRSLFTVSVGGQP-KYSDGFGPKPADIVHVPF-NDLHAVKAVMDDHTC-- 188 Query: 189 ERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGR 248 A+++EP+QGEGG A EF++ LR LCDQH LL+ DEVQ G GR Sbjct: 189 --------------AVVVEPIQGEGGVTAATPEFLQGLRDLCDQHQALLVFDEVQCGMGR 234 Query: 249 TGTFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAA 308 TG+ FA GVT D+ T AK++ GGFP++ + + A G G TY G+P+ACA Sbjct: 235 TGSLFAYMHYGVTPDILTSAKALGGGFPISAMLTTHDIASAFHAGSHGSTYGGNPLACAV 294 Query: 309 ALAVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFENGDSHK 368 A ++ +LD A E V L+ I A++ + ++R +G +I EL K Sbjct: 295 GGAAFDLINTPEVLDGVTAKRELFVQHLQQIDARFDLFSDIRGMGLLIGAEL-------K 347 Query: 369 PNAAAVAQ-VVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLA 416 P A+ + A + G+++L+ G +V+R + L D+ + +G+A Sbjct: 348 PQYHGKARDFLYAAAEAGVMVLNAGP--DVMRFVPSLVIDDSDIAEGMA 394 Lambda K H 0.320 0.137 0.394 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: 448 Number of extensions: 19 Number of successful extensions: 4 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: 425 Length of database: 406 Length adjustment: 31 Effective length of query: 394 Effective length of database: 375 Effective search space: 147750 Effective search space used: 147750 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