Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 6937267 Sama_1437 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >FitnessBrowser__SB2B:6937267 Length = 436 Score = 159 bits (403), Expect = 1e-43 Identities = 118/320 (36%), Positives = 169/320 (52%), Gaps = 31/320 (9%) Query: 12 DFDQVMVPNYAPAAFIPVRGA----GSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAAL 67 D + + P + AA +PV G G R+ + GREL+D + G+ HPALV+A+ Sbjct: 8 DRNHLWHPYTSMAAPLPVLGVQSARGCRLTLEDGRELVDGTSSWWSAIHGYGHPALVSAV 67 Query: 68 TEQANKLWHVS-NVFTNEPALRLAH---KLVDATFAERVFFCNSGAEANEAAFKLARRVA 123 QA KL HV T+EPA L KLV T RVF+ +SG+ A E A K+A + Sbjct: 68 QAQAAKLSHVMFGGLTHEPATALGKALLKLVHPTLT-RVFYADSGSVAVEVALKMAMQYW 126 Query: 124 HDRFGTEKYEIVAALNSFHGRTLFTVNVGGQSKYSDG-FG---PKITGITHVPYN----- 174 R +K++++ L +HG T ++V + G FG PK P Sbjct: 127 QGRSEPQKHKLLTVLGGYHGDTFAAMSVCDPNSGMHGMFGHLVPKQIFAKAPPAGFGRSL 186 Query: 175 ---DLAALKAAVS---DKTCAVVLEPI-QGEGGVLPAELSYLQGARELCDAHNALLVFDE 227 DLA L+A + + A+++EPI QG GG+ YL+ R LCD + LL+ DE Sbjct: 187 AEQDLAELRALLQAHHQEIAALIIEPIMQGAGGLRFHSPDYLKSVRALCDEYRVLLILDE 246 Query: 228 VQTGMGRSGKLFAYQHYGVTPDILTSAKSLGGG-FPIAAMLTTEDLAKHLV-----VGTH 281 + TG GR+GK FAY+H G+TPD+L K+L GG +AA L T+++A + V H Sbjct: 247 IATGFGRTGKAFAYEHAGITPDLLCLGKALTGGMLSLAATLCTDEVAAGISSSPAGVFMH 306 Query: 282 GTTYGGNPLACAVAEAVIDV 301 G T+ NPLACA A A +++ Sbjct: 307 GPTFMANPLACAAALASLEL 326 Lambda K H 0.320 0.136 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: 410 Number of extensions: 15 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: 406 Length of database: 436 Length adjustment: 32 Effective length of query: 374 Effective length of database: 404 Effective search space: 151096 Effective search space used: 151096 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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