Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_043918626.1 jaqu_RS08900 aspartate aminotransferase family protein
Query= reanno::WCS417:GFF4238 (406 letters) >NCBI__GCF_000877395.1:WP_043918626.1 Length = 394 Score = 332 bits (851), Expect = 1e-95 Identities = 182/386 (47%), Positives = 238/386 (61%), Gaps = 9/386 (2%) Query: 20 NYAPAAFIPVRGEGSRVWDQAGRELIDFAGGIAVNVLGHAHPALVGALTEQAHKLWHVSN 79 N AP AF V GEGS + ++ GR +D GIAVNVLGHAHPAL ALT QA +LWH SN Sbjct: 10 NRAPLAF--VSGEGSWLVERGGRRYLDLGAGIAVNVLGHAHPALTEALTAQAGQLWHTSN 67 Query: 80 VFTNEPALRLAHKLIDATFAERVFFCNSGAEANEAAFKLARRVAFDRFGSEKYEIIAALN 139 ++ LA +L++ATFA+ VFF NSG EA E A K+AR+ + G ++ I+A Sbjct: 68 LYEIPQQQELAERLVEATFADTVFFTNSGTEACELAVKMARKY-WSTKGEDRATIVAFTG 126 Query: 140 SFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLDALKAAVS-DKTCAVVLEPIQGE 198 SFHGR+ + G K +DGFGP + G HVP+ D DA + D AV+LEPIQGE Sbjct: 127 SFHGRSSAGIAAAGSKKMTDGFGPLLPGFVHVPFGDHDAFAEVMKRDDIAAVILEPIQGE 186 Query: 199 GGVLPAELAYLQGARDLCDANNALLVFDEVQTGMGRSGHLFAYQHYGVTPDILTSAKSLG 258 GG++P L+G RD+CD AL++ DEVQ GMGR+G LFA++ GVTPDI+ AK +G Sbjct: 187 GGIVPVPDQCLKGLRDVCDRTGALMILDEVQCGMGRTGKLFAHEWAGVTPDIMMVAKGIG 246 Query: 259 GGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLAGVNAKHDLF 318 GGFP+ A+L TE A + GTHG+TYGGNPLACAV AV++V+ LA V K L Sbjct: 247 GGFPLGALLATEHAAAGMSAGTHGSTYGGNPLACAVGNAVMEVVADEAFLAEVRRKAGLL 306 Query: 319 KARLE-QIGKQYGIFTEVRGMGLLLGCVLSDAFKGKAKDVFNAAEKENLMILQAGPDVVR 377 + LE + +F VRG GL+LG + DV AA ++I+ A + R Sbjct: 307 RQGLEGLVASHPDVFEVVRGSGLMLGL----KCRVPVGDVIAAARDAEVLIVPAADETAR 362 Query: 378 FAPSLVVEDADIKEGLDRFERAVKAL 403 P+L + D DI+E LDR +RA A+ Sbjct: 363 LLPALNIGDDDIREALDRLDRAAAAV 388 Lambda K H 0.320 0.137 0.400 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: 443 Number of extensions: 18 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 406 Length of database: 394 Length adjustment: 31 Effective length of query: 375 Effective length of database: 363 Effective search space: 136125 Effective search space used: 136125 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 24 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