Align 4-aminobutyrate aminotransferase; EC 2.6.1.19 (characterized, see rationale)
to candidate 642684930 Cphamn1_2453 adenosylmethionine-8-amino-7-oxononanoate aminotransferase apoenzyme (EC 2.6.1.62)
Query= uniprot:A1S8Y2 (425 letters) >IMG__ChlphaBS1_FD:642684930 Length = 434 Score = 165 bits (417), Expect = 3e-45 Identities = 124/357 (34%), Positives = 176/357 (49%), Gaps = 31/357 (8%) Query: 25 PVFTERAENATVWDVE-GREYIDFAGGIAVLNTGHLHPKVKAAVAEQLEKFSHTCFMVLG 83 PV+ + + ++E GR ID G+ HP + AV +QLEK SH F Sbjct: 27 PVYPVKGASGVRIELEDGRRLIDGMSSWWAAIHGYNHPVLNEAVRKQLEKMSHVMFGGFT 86 Query: 84 YESYVAVCEKLNQLVPGDFAKKSALFTSGSEAVENAIKVARAYTKRAG------VIAFTS 137 +E V + EKL L PG +K SGS +VE AIK+A Y AG ++ S Sbjct: 87 HEPAVRLAEKLVDLTPGPL-QKVFFSDSGSVSVEVAIKMALQYHHAAGRPKKNRLLTIRS 145 Query: 138 GYHGRTMAALALTGKVAP-YSKGMGLMQANVFRAEFPCALHGVSEDDAMASIERIFKNDA 196 GYHG T AA+++ V + G++ +F C H V DD++ R + + Sbjct: 146 GYHGDTFAAMSVCDPVTGMHGLFSGVLPQQLFAEAPACGFHDVWSDDSIGDFRR--QVEM 203 Query: 197 EPSDIAAIILEPV-QGEGGFYAATPGFMKRLRELCDREGIMLIADEVQTGAGRTGTFFAM 255 +IAA+ILEPV QG GG +P ++ R+RELCDR ++LI DE+ TG GRTG FA+ Sbjct: 204 YHREIAAVILEPVVQGAGGMRFYSPEYLVRVRELCDRYDLLLIFDEIATGFGRTGKMFAL 263 Query: 256 EQMGVAADITTFAKSIAGGF----------PLSGITGRAEVMDAIGPGGL--GGTYGGSP 303 E V DI K++ GG+ +SG+ AE PG G T+ +P Sbjct: 264 EHADVVPDILCIGKALTGGYMTLAATLTNGDVSGVISNAE------PGVFMHGPTFMANP 317 Query: 304 LACAAALAVIEVFEEEKLLERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIEL 360 LACA A A I++ E I + S + E P +A+VR LG++ +EL Sbjct: 318 LACAVASASIDLLAESDWRNSVRVIEAQLASGL-EPCRIVPGVADVRVLGAIGVVEL 373 Lambda K H 0.319 0.136 0.391 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: 421 Number of extensions: 26 Number of successful extensions: 7 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: 434 Length adjustment: 32 Effective length of query: 393 Effective length of database: 402 Effective search space: 157986 Effective search space used: 157986 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 Apr 09 2024. 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