Align Succinylornithine transaminase; SOAT; Succinylornithine aminotransferase; EC 2.6.1.81 (characterized)
to candidate N515DRAFT_1751 N515DRAFT_1751 adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= SwissProt::Q8ZPV2 (408 letters) >FitnessBrowser__Dyella79:N515DRAFT_1751 Length = 467 Score = 169 bits (428), Expect = 2e-46 Identities = 139/421 (33%), Positives = 200/421 (47%), Gaps = 46/421 (10%) Query: 22 PFIP-VRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPALREALNEQANRFWH-IGNGYT 79 P +P VRGEG L D G+ Y+D N GHA+P + AL +Q + H I G+T Sbjct: 46 PMLPIVRGEGPWLVDADGRRYLDGISSWWTNLFGHANPRIGAALKQQLDTLEHVIFAGFT 105 Query: 80 NEPALRLAKKLIDATFA--ERVFFCNSGAEANEAALKLARKYAHDRVGNHKSGIVAFKNA 137 +EPA+ LA++L T A ERVF ++G+ A E ALK++ Y ++ K+ +A + Sbjct: 106 HEPAIELAERLAQITPAGLERVFLADNGSAAIEVALKMSFHYWLNQGAGQKTRFIALTGS 165 Query: 138 FHGRTLFTVSAGGQPTYSQDFAPL--------PPDIRHA---------AYNDLNSASALI 180 +HG TL +S Y + +APL PD A A L L+ Sbjct: 166 YHGETLGALSVSDVALYRKTYAPLLLTPVLAPSPDAYEAEPGESAEACAARRLGELRVLL 225 Query: 181 DDN---TCAVIVEP-VQGEGGVIPATKAFLQGLRELCDRHQALLIFDEVQTGVGRTGELY 236 + + TCAVIVEP VQ GG+ ++L GLR LCD I DE+ G GRTG L+ Sbjct: 226 EQHAHETCAVIVEPLVQCAGGMRMYHPSYLTGLRALCDEFGVHFIADEIAVGFGRTGTLF 285 Query: 237 AYMHYGVTPDILTTAKALGGGF-PIGAMLTT----QDYASVMTPG---THGTTYGGNPLA 288 A GV+PD + +K L GGF P+ A+LTT + + + G H +Y GNPLA Sbjct: 286 ACEQAGVSPDFMCLSKGLTGGFLPLSAVLTTTPVYEAFYAEYNAGKAFLHSHSYTGNPLA 345 Query: 289 TAVAGKVLDIINTPEMQNGVRQRHDAFIERLNTLNVRFGMFSEIRGLGLLLGCVLQTEFA 348 A LDI + R+ RL L +++R G++ L + A Sbjct: 346 CRAALATLDIFRDEPVLERNRELAAHLARRLAPLR-EHPQVADVRQTGMIAAVELVRDKA 404 Query: 349 GKAKLIAQEAAKAGVMVLIAG----------GDVVRFAPALNVSDEEIATGLDRFALACE 398 +A ++E + G+ V + G G+VV F P VS +E+ +D E Sbjct: 405 TRAPYPSEE--RRGLRVYLHGLEHGALLRPLGNVVYFMPPYVVSTDELDHLVDVAIAGIE 462 Query: 399 R 399 R Sbjct: 463 R 463 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: 492 Number of extensions: 26 Number of successful extensions: 6 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: 467 Length adjustment: 32 Effective length of query: 376 Effective length of database: 435 Effective search space: 163560 Effective search space used: 163560 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