Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_245779653.1 BM299_RS04985 aspartate aminotransferase family protein
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_900115975.1:WP_245779653.1 Length = 471 Score = 204 bits (520), Expect = 3e-57 Identities = 134/403 (33%), Positives = 207/403 (51%), Gaps = 37/403 (9%) Query: 29 VRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHV--SNVFTNEPA 86 VR EG+RVWD G +DF GG ++GH HP +++A+ EQ + + ++ +++ T A Sbjct: 55 VRAEGTRVWDSEGNAYLDFLGGYGSLNIGHNHPRVIEAV-EQVRELPNILQASIPTITAA 113 Query: 87 LRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAASNSFHGRTL 146 L ++ +R FL NSGAEA E A KLAR + I NSFHG++ Sbjct: 114 LLHNLAVITPGKLKRSFLCNSGAEAVEGALKLARAATG------RKTFIYCRNSFHGKSF 167 Query: 147 FTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISD-KTCAVVLEPIQGEGGVLPAQ 205 ++V G+ KY + F P VP+ D++AL+ A+ + A ++EP+QGEGG+ Sbjct: 168 GALSVTGREKYRELFEPLLFDCREVPFGDIDALRKALRKYQAAAFIVEPVQGEGGINMPP 227 Query: 206 QAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPDILSSAKSLGGG-FPIG 264 + YL A + C + L + DE+Q+G GR G +FA H V PD++ AKSLGGG PIG Sbjct: 228 RGYLSEAARACRDAGTLFIADEIQTGFGRTGAMFACQHENVEPDVMCLAKSLGGGIMPIG 287 Query: 265 AMLTTGEIAKHL-----SVGTHGTTYGGNPLASAVAEAALDVINTPEVLDGVKAKHERFK 319 A +T +I + H +T+GGN A+A AA++V+ ++ K F Sbjct: 288 AFITNDDIWQKAYGSVEKATLHTSTFGGNTWAAAAGIAAIEVLVKEKLPAAAAEKGTYFI 347 Query: 320 SRLQKIGQEYGIFDEIRGMGLLIG------------------AALTDEWKGK--ARDVLN 359 S L+ + ++Y + E+RG GLLIG + L+ E+ G A ++LN Sbjct: 348 SGLRDLQKKYPLLQEVRGQGLLIGIELAQPGGLTNKATMGLASKLSHEYLGSMVAGELLN 407 Query: 360 AAEKEAVMVLQASPDVVRFAPSLVIDDAEIDEGLERFERAVAK 402 L +P+V+R P L + E+D L + + K Sbjct: 408 RHRIITAYTLN-NPNVIRMEPPLTVTGEELDYVLNALDDVLKK 449 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: 458 Number of extensions: 27 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: 406 Length of database: 471 Length adjustment: 32 Effective length of query: 374 Effective length of database: 439 Effective search space: 164186 Effective search space used: 164186 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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