Align ornithine transaminase Car2; EC 2.6.1.13 (characterized)
to candidate WP_092350113.1 BLU87_RS14535 glutamate-1-semialdehyde-2,1-aminomutase
Query= CharProtDB::CH_125889 (438 letters) >NCBI__GCF_900107645.1:WP_092350113.1 Length = 427 Score = 126 bits (316), Expect = 1e-33 Identities = 101/319 (31%), Positives = 159/319 (49%), Gaps = 35/319 (10%) Query: 32 PVCFSKAKGAKVWDPEGREYLDFLSAYSAVNQGHCHPKIIEALVEQAQRVTLSSRAFYND 91 P+ +KA G+K++D +G EY+D++ ++ + GHCHPK++EA+ Q+ S +F Sbjct: 35 PIFIAKAAGSKIYDVDGNEYIDYVGSWGPMILGHCHPKVVEAI----QKTAASGASFGAP 90 Query: 92 KFGPFAKYITE-----YFGYEMVIPMNTGAEAVETACKLARLWGYKAKKIPTDEAIILSC 146 P + E Y E V +++G EA +A +LAR GY T IL Sbjct: 91 T--PLETELAEIVCEAYPNIEKVRMVSSGTEATMSAIRLAR--GY------TGRDKILKF 140 Query: 147 VDNFHGRTMGIISMSTDPDARDNYG-PYLPNVGPKISGADRVLRYNNIEDLKYYLDTFGP 205 +HG ++ + A +G P P V + YN++ +++ + Sbjct: 141 DGCYHGHADSLLVKAGSGLA--TFGVPTSPGVPADFAKYTLTANYNDLANVQELVAANKG 198 Query: 206 KVAAFLVEPIQGEAGVMVPDDGYLEEAYKLCKAHNVLFIADEVQTG--VARTGKMLCIEH 263 ++A ++E + G G + P G+L+E LC A ++ I DEV TG VA G E Sbjct: 199 EIACIILEAVAGNMGCVPPVKGFLQELRDLCTAEGIILIIDEVMTGFRVAYGGAQ---ER 255 Query: 264 SNVKPDVVILGKAISGGVYPVSAVLSSREIM--LNFEPGTH-GSTYGGNPLGAAVSIAAL 320 V+ D+V LGK I GG+ PV A REIM L+ E G + T GNPL + IA L Sbjct: 256 FGVRGDLVCLGKIIGGGL-PVGAFGGKREIMDSLSPEGGVYQAGTLSGNPLAMSAGIATL 314 Query: 321 EVVKEE----KLTERAAVL 335 +++++E +L E+AA L Sbjct: 315 KLLQQEGFYQQLEEKAAYL 333 Lambda K H 0.318 0.136 0.402 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: 440 Number of extensions: 25 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: 438 Length of database: 427 Length adjustment: 32 Effective length of query: 406 Effective length of database: 395 Effective search space: 160370 Effective search space used: 160370 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