Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate GFF2666 Psest_2719 acetylornithine and succinylornithine aminotransferases/succinylornithine transaminase family
Query= metacyc::MONOMER-11537 (425 letters) >FitnessBrowser__psRCH2:GFF2666 Length = 406 Score = 204 bits (520), Expect = 3e-57 Identities = 145/415 (34%), Positives = 207/415 (49%), Gaps = 40/415 (9%) Query: 23 IHPIFADSA------KNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTH 76 I P FA +A + V D GRE +DFAGGIAV GH HP ++AA+TEQ KL H Sbjct: 17 IVPTFAPAAFVPVRGLGSRVWDQSGRELVDFAGGIAVNALGHAHPAMVAALTEQAGKLWH 76 Query: 77 TCFQVLAYEPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARA------ATGRA 130 + EP + L +K+ V FA + +G+EA E A K+AR + Sbjct: 77 IS-NIYTNEPALRLAKKL---VAATFADRAFFCNSGAEANEAAFKLARRYAHDVYGPQKF 132 Query: 131 GVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIER 190 +I+ ++HGRT+ T+ + G+ YS G G GI Y N+L + S + Sbjct: 133 EIISALNSFHGRTLFTVTVGGQS-KYSDGFGPKIEGITHVPY-NDLEALKAAISDKT--- 187 Query: 191 IFKNDAEPRDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTG 250 A+++EP+QGE G + +++ R LC++H LLI DEVQTG GRTG Sbjct: 188 -----------CAVVLEPIQGESGILPGEQAYLEGARQLCNEHNALLIFDEVQTGMGRTG 236 Query: 251 TFFAMEQMGVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAAL 310 FA G+T D+ T AKS+ GGFP+ + E ++ G G TY G+P+ACA A Sbjct: 237 ELFAYMHYGITPDILTNAKSLGGGFPIGAMLTTNEIAAHLSVGTHGTTYGGNPLACAVAE 296 Query: 311 AVMEVFEEEHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFENGDSHKPN 370 AV+++ +L+ KA ER L I +Y V VR G +I L D+ K Sbjct: 297 AVVDIVNTPEVLEGVKAKHERFKARLTQIGERYGVFSLVRGRGLLIGCVL---SDAWKGK 353 Query: 371 AAAVAQVVAKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEECFAEL 425 A A A A + L++L G +V+R+ L A +D+GL +E A L Sbjct: 354 AGAFC---AAAEKEALMVLQAGP--DVVRLAPSLVIDQADIDEGLDRLERAVAAL 403 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: 404 Number of extensions: 16 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 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