Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate Ac3H11_4342 Omega-amino acid--pyruvate aminotransferase (EC 2.6.1.18)
Query= SwissProt::Q8ZPV2 (408 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4342 Length = 454 Score = 146 bits (368), Expect = 1e-39 Identities = 127/402 (31%), Positives = 189/402 (47%), Gaps = 39/402 (9%) Query: 22 PFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWHIGNGYTNE 81 P + V G+G+ D G++ D G+ + LGH + EA+ + A + Sbjct: 40 PRMIVSGQGAYYTDADGRKIFDGLSGLWCSGLGHGRKDVAEAIGKAAATLDYSPAFQFGH 99 Query: 82 PA-LRLAKKLIDATFA--ERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNAF 138 PA LA KL + T A + VFF SG+E+ + +LK+AR Y + K+ ++ + + Sbjct: 100 PASFALANKLKELTPAGLDYVFFTGSGSESADTSLKMARAYWRAKGQASKTRLIGREKGY 159 Query: 139 HGRTLFTVSAGG----QPTYSQ----DFAP--LPP----------DIRHAAYNDLNSASA 178 HG +S GG + T+ Q D P PP D A + L A Sbjct: 160 HGVNYGGISVGGIVGNRKTFGQGIEADHLPHTQPPAGTFQKGMAEDGGRALADKLLDVIA 219 Query: 179 LID-DNTCAVIVEPVQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELYA 237 L D N AVIVEP G GV+ K +L+ +RE+C ++ LLIFDEV TG GR G Sbjct: 220 LHDASNIAAVIVEPFSGSAGVVIPPKGYLERIREICTQNNILLIFDEVITGFGRCGAWTG 279 Query: 238 YMHYGVTPDILTTAKAL-GGGFPIGAMLTTQD-YASVMTPG--------THGTTYGGNPL 287 +GVTPDIL AK + G P+G ++ T++ Y + ++ G HG TY +P+ Sbjct: 280 AEAFGVTPDILNFAKQVTNGAQPLGGVIATKEIYDTFISQGGPEYMLEFPHGYTYSAHPV 339 Query: 288 ATAVAGKVLDIINTPEMQNGVRQRHDAFIERLNTLNVRFGMFSEIRGLGLLLG---CVLQ 344 A A VLDI+ +M V+ F ++ L + ++IR GL G L Sbjct: 340 ACAAGNAVLDILQKEDMPGRVKALAPHFENAVHGLKGAKHV-ADIRNYGLAAGITISALP 398 Query: 345 TEFAGKAKLIAQEAAKAGVMVLIAGGDVVRFAPALNVSDEEI 386 +E A + IA + + G V GGD ++ AP + EI Sbjct: 399 SEPAKRPYEIAMKCWEKGFYVRY-GGDTIQLAPPFISTSAEI 439 Lambda K H 0.320 0.137 0.413 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: 473 Number of extensions: 25 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: 408 Length of database: 454 Length adjustment: 32 Effective length of query: 376 Effective length of database: 422 Effective search space: 158672 Effective search space used: 158672 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 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