Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 6937472 Sama_1628 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= BRENDA::O30508 (406 letters) >FitnessBrowser__SB2B:6937472 Length = 405 Score = 526 bits (1356), Expect = e-154 Identities = 256/397 (64%), Positives = 314/397 (79%) Query: 8 VERADFDRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKAL 67 + R+ FD MVPNYAP+ IPV+G GSR+WDQ GRE IDFAGGIAV LGH HPALV AL Sbjct: 3 INRSLFDEVMVPNYAPSPIIPVKGLGSRLWDQQGREFIDFAGGIAVNCLGHCHPALVSAL 62 Query: 68 TEQAQRIWHVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVY 127 TEQAQ++WH+SN TNEPAL LA+ LVD TFAE+V+ ANSGAEANEAA KL RR A + + Sbjct: 63 TEQAQKLWHLSNTMTNEPALMLAKHLVDNTFAEKVYFANSGAEANEAALKLVRRVALNKF 122 Query: 128 GPQKYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKT 187 G K +IIA FHGRTLFTV+VGGQP YSDGFGPK I H YN+L++LKA ISD+T Sbjct: 123 GADKSQIIAFKQGFHGRTLFTVSVGGQPAYSDGFGPKPADIDHAEYNNLDSLKALISDRT 182 Query: 188 CAVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVV 247 CAVVLEP+QGEGG++ +++G R+LCD+HNALLVFDEVQ+G+GR GEL+AYM GV Sbjct: 183 CAVVLEPLQGEGGIINPTPEFIKGVRELCDQHNALLVFDEVQTGVGRTGELYAYMGLGVT 242 Query: 248 PDILSSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEV 307 PD+L++AK+LGGGFPIGAMLTT E+AKHL VGTHG+TYGGNPLA AV AA +NTPEV Sbjct: 243 PDVLTTAKALGGGFPIGAMLTTTELAKHLVVGTHGSTYGGNPLACAVGLAAFTTVNTPEV 302 Query: 308 LDGVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVM 367 L+GVK + + F+ L I +Y +F E+RG GLL+GAAL ++ GKARD + AA +E V+ Sbjct: 303 LNGVKEREQLFRDGLNAINDKYQVFTEVRGKGLLLGAALNADYAGKARDFMLAAAEEGVL 362 Query: 368 VLQASPDVVRFAPSLVIDDAEIDEGLERFERAVAKLV 404 +L A +VVRFAPSL+I +A++ EGL RF+ A+AKLV Sbjct: 363 LLMAGQNVVRFAPSLIIPEADVREGLARFDAAIAKLV 399 Lambda K H 0.318 0.135 0.394 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: 527 Number of extensions: 12 Number of successful extensions: 1 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: 405 Length adjustment: 31 Effective length of query: 375 Effective length of database: 374 Effective search space: 140250 Effective search space used: 140250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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