Align ornithine aminotransferase (characterized)
to candidate WP_086508434.1 BZY95_RS02535 aspartate aminotransferase family protein
Query= CharProtDB::CH_124176 (442 letters) >NCBI__GCF_002151265.1:WP_086508434.1 Length = 450 Score = 167 bits (424), Expect = 5e-46 Identities = 134/431 (31%), Positives = 207/431 (48%), Gaps = 45/431 (10%) Query: 45 ARAQGVNVWDPEGKHYLDLLSAYSAVNQGHCHPELIKALAEQAGRLTLSSRAFYNDVFPV 104 + A+GV +WD G+ YLD S + N GH ++ +A+ Q R+ + R + + V Sbjct: 18 SHAKGVYLWDETGRQYLDGCSGAISCNLGHGRNDIREAMLAQLDRVAFTYRTQFENAPAV 77 Query: 105 WAAKVRDLFGY-----DMVLPMNTGAEAVETAIKIARKWAYKVKGVPQGKAHVFSVADNF 159 AK L G+ + V +++G+EAVE+A+K+AR++ + +G PQ + V S+ ++ Sbjct: 78 ALAKA--LVGFTQQQLEKVFFVSSGSEAVESALKLARQY-FVARGEPQRRRFV-SLRPSY 133 Query: 160 HGRTMTAISLS-TDPESRDNYGPYVPNIGAICP--------TTGRQIRYNNISDLEIVLE 210 HG T+ A+ ++ P + ++ P GR + ++D +E Sbjct: 134 HGSTLGALGVTGYQPLEAPFRDIAIGSLKVAGPDFYRHDDTDDGRHVA-RVLADTRAAIE 192 Query: 211 AHGAET-AAFIVEPIQG-EAGVVVPDDDYLAKVHALCKKHNVLFICDEIQTGIARTGKML 268 A G +T AAF++EP+ G G D YLA + ALC + L I DE+ TGI RTG Sbjct: 193 AAGPDTIAAFVLEPVGGASTGARKLDRSYLAGIRALCDEFGCLLILDEVLTGIGRTGTWF 252 Query: 269 CCNWAGIKPDIVTLGKAISGGMYPVSCVLADKDVMMVVEPG---THGSTYGGNPLGCAVS 325 G+ PD+++ K + G YPV VL+ D++ V HG TY GNPL CA Sbjct: 253 AYQHYGVTPDLLSTAKGLGAGYYPVGAVLSRADIVETVMASGGFQHGHTYAGNPLACATG 312 Query: 326 IRALELVEEGKLADQADHLGRIFREGVEAFKS--PIVQQVRGKGLLNAVVIDESAAG--- 380 + +E +E K+ D GR G+EA K+ P V VRG GLL V + AA Sbjct: 313 LAVVEAIEREKILDNVAARGRQLAAGLEALKARFPWVGDVRGLGLLWGVELVADAASKAP 372 Query: 381 -----GRTAWDLCMLLKSKGLLAKPTH------GNIIRFAPPLIITEEELKKALSIIGEA 429 R A + L + +GLL P G+ PPL I + + L+ + A Sbjct: 373 FPAEQNRFA-RITALAREEGLLIYPRRTLDGIAGDHFLITPPLTIDAADTAELLTRLERA 431 Query: 430 L----TELPTA 436 + E+P A Sbjct: 432 MQRFDREVPAA 442 Lambda K H 0.318 0.135 0.404 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: 444 Number of extensions: 28 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 442 Length of database: 450 Length adjustment: 32 Effective length of query: 410 Effective length of database: 418 Effective search space: 171380 Effective search space used: 171380 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 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