Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_086510803.1 BZY95_RS15480 4-aminobutyrate--2-oxoglutarate transaminase
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_002151265.1:WP_086510803.1 Length = 430 Score = 222 bits (566), Expect = 1e-62 Identities = 142/411 (34%), Positives = 210/411 (51%), Gaps = 34/411 (8%) Query: 22 APAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTEQAQRIWHV-SNV 80 +PA R E + +WD G +IDFAGGI V ++GH HP +V+A+ Q ++ H V Sbjct: 20 SPATQFADRAENALIWDADGNRIIDFAGGIGVLNIGHRHPKVVEAVKAQLDKVMHTCQTV 79 Query: 81 FTNEPALRLARKLVDATFAE---RVFLANSGAEANEAAFKLARRYANDVYGPQKYEIIAA 137 E +++A KL T +V LANSGAEA E A K+AR K +I Sbjct: 80 MPYEGYVKVAEKLSQVTPVRGHAKVMLANSGAEALENAVKIARAATG------KNNVICF 133 Query: 138 SNSFHGRTLFTVNVGGQ-PKYSDGFGPKFEGITHVPY----------NDLEALKAAISDK 186 +HGRT T+ + G+ Y+ FG + PY + LK AI Sbjct: 134 DGGYHGRTFMTMAMNGKVAPYASDFGTMPGNVFRAPYPVPYHGVSEDEAIRGLKMAIKTD 193 Query: 187 -----TCAVVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAY 241 T A+VLEP+ GEGG PA ++L+ R++CDEH L++ DEVQSG GR G+LFA Sbjct: 194 ANPRDTAAIVLEPVLGEGGFYPAPASFLKAIREICDEHGMLMIVDEVQSGFGRTGKLFAI 253 Query: 242 MHYGVVPDILSSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDV 301 H GV PDI++ AKS+ G PI A++ T ++ + G TY GNPL+ A A LDV Sbjct: 254 EHSGVEPDIITMAKSMADGMPISAVVGTDKVMDASGPNSLGGTYTGNPLSCAATLAVLDV 313 Query: 302 INTPEVLDGVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAAL-TDEWK-----GKAR 355 +L+ A ++ R + +++ D R MG + L TD+ K A Sbjct: 314 FEEENILEKSMALGDKLAKRFAQWQRDFDCVDNARNMGAMAALDLVTDKAKHTPDADLAA 373 Query: 356 DVLNAAEKEAVMVLQAS--PDVVRFAPSLVIDDAEIDEGLERFERAVAKLV 404 + A ++ +++L + +RF + I+D ++EGL+ E A+ +LV Sbjct: 374 ALCKKAREKGLILLSCGLYGNTIRFLMPVTIEDEILEEGLDIVEAALTELV 424 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: 447 Number of extensions: 15 Number of successful extensions: 5 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: 430 Length adjustment: 32 Effective length of query: 374 Effective length of database: 398 Effective search space: 148852 Effective search space used: 148852 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 Apr 10 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