Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 6938533 Sama_2636 4-aminobutyrate aminotransferase (RefSeq)
Query= BRENDA::A0A140N9B6 (406 letters) >FitnessBrowser__SB2B:6938533 Length = 425 Score = 216 bits (550), Expect = 1e-60 Identities = 140/402 (34%), Positives = 210/402 (52%), Gaps = 31/402 (7%) Query: 22 PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPELREALNEQASKFWHTGN---GY 78 P R E + +WD +G+EYIDFAGGIAV GH HP+++ A+ EQ KF HT GY Sbjct: 25 PVFTERAENATVWDVEGREYIDFAGGIAVLNTGHLHPKVKAAVAEQLEKFSHTCFMVLGY 84 Query: 79 TNE-PVLRLAKKLIDATFADRVFFCNSGAEANEAALKLARKFAHDRYGSHKSGIVAFKNA 137 + V +L+ FA + SG+EA E A+K+AR + + ++G++AF + Sbjct: 85 ESYVAVCEKLNQLVPGDFAKKSALFTSGSEAVENAIKVARAY------TKRAGVIAFTSG 138 Query: 138 FHGRTLFTVSAGGQPA-YSQDFAPLPADIRHA----AYNDINSASALID----------- 181 +HGRT+ ++ G+ A YS+ + A++ A A + ++ A+ Sbjct: 139 YHGRTMAALALTGKVAPYSKGMGLMQANVFRAEFPCALHGVSEDDAMASIERIFKNDAEP 198 Query: 182 DSTCAVIVEPIQGEGGVVPASNAFLQGLRELCNRHNALLIFDEVQTGVGRTGELYAYMHY 241 A+I+EP+QGEGG A+ F++ LRELC+R +LI DEVQTG GRTG +A Sbjct: 199 SDIAAIILEPVQGEGGFYAATPGFMKRLRELCDREGIMLIADEVQTGAGRTGTFFAMEQM 258 Query: 242 GVTPDLLTTAKALGGGFPVGALLATEECARVMTVGTHGTTYGGNPLASAVAGKVLELINT 301 GV D+ T AK++ GGFP+ + E + G G TYGG+PLA A A V+E+ Sbjct: 259 GVAADITTFAKSIAGGFPLSGITGRAEVMDAIGPGGLGGTYGGSPLACAAALAVIEVFEE 318 Query: 302 PEMLNGVKQRHDWFVERLNTINHRYGLFSEVRGLGLLIGCVL--NADYAGQ-AKQISQEA 358 ++L + + RY +EVRGLG +I L N A + Q+ EA Sbjct: 319 EKLLERSNAIGQTIKSAIGELASRYPQIAEVRGLGSMIAIELMENGKPAPEYCPQVLTEA 378 Query: 359 AKAGVMVLIAG--GNVVRFAPALNVSEEEVTTGLDRFAAACE 398 G+++L G GNV+R + +E++ GL+ A E Sbjct: 379 RNRGLILLSCGTYGNVLRILVPITAPDEQIQRGLEIMAECFE 420 Lambda K H 0.319 0.135 0.406 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: 447 Number of extensions: 14 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: 406 Length of database: 425 Length adjustment: 31 Effective length of query: 375 Effective length of database: 394 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 Aug 03 2021. The underlying query database was built on Aug 03 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