Align 4-aminobutyrate transaminase subunit (EC 2.6.1.19) (characterized)
to candidate 6937472 Sama_1628 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= metacyc::MONOMER-11537 (425 letters) >FitnessBrowser__SB2B:6937472 Length = 405 Score = 225 bits (573), Expect = 2e-63 Identities = 146/407 (35%), Positives = 208/407 (51%), Gaps = 34/407 (8%) Query: 25 PIFADSAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAY 84 PI + + D +GREFIDFAGGIAV GH HP +++A+TEQ KL H + Sbjct: 20 PIIPVKGLGSRLWDQQGREFIDFAGGIAVNCLGHCHPALVSALTEQAQKLWHLS-NTMTN 78 Query: 85 EPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARAAT------GRAGVIAFTGA 138 EP + L + + V FA+K +G+EA E A+K+ R ++ +IAF Sbjct: 79 EPALMLAKHL---VDNTFAEKVYFANSGAEANEAALKLVRRVALNKFGADKSQIIAFKQG 135 Query: 139 YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALYPNELHGVSIDDSIASIERIFKNDAEP 198 +HGRT+ T+ + G+ YS G G P I A Y N + S++ + + Sbjct: 136 FHGRTLFTVSVGGQPA-YSDGFGPKPADIDHAEYNN----------LDSLKALISDRT-- 182 Query: 199 RDIAAIIIEPVQGEGGFYVAPKEFMKRLRALCDQHGILLIADEVQTGAGRTGTFFAMEQM 258 A+++EP+QGEGG EF+K +R LCDQH LL+ DEVQTG GRTG +A + Sbjct: 183 ---CAVVLEPLQGEGGIINPTPEFIKGVRELCDQHNALLVFDEVQTGVGRTGELYAYMGL 239 Query: 259 GVTADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEE 318 GVT D+ T AK++ GGFP+ + E + G G TY G+P+ACA LA Sbjct: 240 GVTPDVLTTAKALGGGFPIGAMLTTTELAKHLVVGTHGSTYGGNPLACAVGLAAFTTVNT 299 Query: 319 EHLLDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFENGDSHKPNAAAVAQVV 378 +L+ K + GL AI KY V EVR G ++ L N D A + Sbjct: 300 PEVLNGVKEREQLFRDGLNAINDKYQVFTEVRGKGLLLGAAL--NAD----YAGKARDFM 353 Query: 379 AKARDKGLILLSCGTYGNVLRVLVPLTSPDAQLDKGLAIIEECFAEL 425 A ++G++LL G NV+R L P+A + +GLA + A+L Sbjct: 354 LAAAEEGVLLLMAGQ--NVVRFAPSLIIPEADVREGLARFDAAIAKL 398 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: 427 Number of extensions: 21 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: 425 Length of database: 405 Length adjustment: 31 Effective length of query: 394 Effective length of database: 374 Effective search space: 147356 Effective search space used: 147356 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