Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 7025943 Shewana3_3091 4-aminobutyrate aminotransferase (RefSeq)
Query= reanno::pseudo6_N2E2:Pf6N2E2_4013 (425 letters) >FitnessBrowser__ANA3:7025943 Length = 425 Score = 609 bits (1571), Expect = e-179 Identities = 306/422 (72%), Positives = 348/422 (82%), Gaps = 3/422 (0%) Query: 1 MSKTNADLMARRTAAVPRGVGQIHPIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVH 60 MS TN LMARR AAV GVGQIHP+F A+NATV DVEGREFIDFAGGIAVLNTGH+H Sbjct: 1 MSTTNDSLMARRQAAVAGGVGQIHPVFTARAENATVWDVEGREFIDFAGGIAVLNTGHLH 60 Query: 61 PKIIAAVTEQLNKLTHTCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAV 120 PK+ AAV QL +HTCF VL YE Y+++CEK+N VPGDFAKKT L T+GSEAVENAV Sbjct: 61 PKVKAAVAAQLEDFSHTCFMVLGYESYIQVCEKLNQLVPGDFAKKTALFTSGSEAVENAV 120 Query: 121 KIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVS 180 K+ARA T RAGVIAFT YHGRTM L LTGKV PYS GMGLM +FRA +P LHGVS Sbjct: 121 KVARAYTKRAGVIAFTSGYHGRTMAALALTGKVAPYSKGMGLMSANVFRAEFPCALHGVS 180 Query: 181 IDDSIASIERIFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIAD 240 DD++ASIERIFKNDAEP +IAAII+EPVQGEGGFY A EFM+RLRALCD+ GI+LIAD Sbjct: 181 DDDAMASIERIFKNDAEPSNIAAIILEPVQGEGGFYAASPEFMQRLRALCDREGIMLIAD 240 Query: 241 EVQTGAGRTGTFFAMEQMGVAADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYA 300 EVQTGAGRTGTFFAMEQMGV+AD+TTFAKSIAGGFPL+G+ GKAE MDAI PGGLGGTY Sbjct: 241 EVQTGAGRTGTFFAMEQMGVSADITTFAKSIAGGFPLSGITGKAEVMDAIGPGGLGGTYG 300 Query: 301 GSPIACAAALAVMEVFEEEHLLDRCKAVGERLVAGLKAIQKKYPVIGDVRALGAMIAVEL 360 G+P+ACAAALAV+EVFEEE LL+R A+GER+ + L +Q ++P I DVR LGAMIA+EL Sbjct: 301 GNPLACAAALAVLEVFEEEKLLERANAIGERIKSALNTMQVEHPQIADVRGLGAMIAIEL 360 Query: 361 FENGDSHKPNAAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTAPDEQLDKGLAILEE 420 E G KP AQ++A+AR++GLILLSCGTYGNVLR+LVPLT PDEQL GL IL+ Sbjct: 361 MEEG---KPAPQYCAQILAEARNRGLILLSCGTYGNVLRILVPLTVPDEQLAAGLGILKS 417 Query: 421 CF 422 CF Sbjct: 418 CF 419 Lambda K H 0.320 0.137 0.395 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: 666 Number of extensions: 18 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: 425 Length of database: 425 Length adjustment: 32 Effective length of query: 393 Effective length of database: 393 Effective search space: 154449 Effective search space used: 154449 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 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