Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_009544618.1 CCE_RS12755 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q8YMS6 (388 letters) >NCBI__GCF_000017845.1:WP_009544618.1 Length = 390 Score = 563 bits (1452), Expect = e-165 Identities = 283/386 (73%), Positives = 329/386 (85%), Gaps = 2/386 (0%) Query: 1 MKLAARVSQVTPSITLAIAAKAKAMKAEGIDVCSFSAGEPDFDTPAHIKAAAAKALDEGK 60 ++LA RV+QVTPS+TLAI AKAK MKA+GIDVCSFS+GEPDFDTP HIK AA+ AL +GK Sbjct: 2 IQLATRVTQVTPSLTLAITAKAKEMKAQGIDVCSFSSGEPDFDTPQHIKEAASSALAQGK 61 Query: 61 TKYGAAAGEPKLREAIARKLQKDNHLDYKPENVIVTNGGKHSLYNLIVALIDPGDEVIIP 120 TKYG AGEP LR+AIA KL +DN L+Y +++IVTNGGKHSL+NL++ALID GDEVIIP Sbjct: 62 TKYGPVAGEPGLRQAIAHKLNQDNQLNYSADHIIVTNGGKHSLFNLMLALIDKGDEVIIP 121 Query: 121 APYWLSYPEMVTLVGGKSVIVPTDASTGYKITPEQLRKAITPKTKLFVLNSPSNPTGMVY 180 APYWLSYPEMV L G VIV T A T YKITPEQLR+AIT TKL VLNSPSNPTGMVY Sbjct: 122 APYWLSYPEMVKLAEGTPVIVNTTAETDYKITPEQLRQAITSNTKLLVLNSPSNPTGMVY 181 Query: 181 TPEEIKALAQVVVDADIYVVSDEIYEKILYDGAQHISIGSLGKEIFNRTLISNGFAKAYS 240 EEIKALA+VVVD +++VVSDEIYEKILYDG +HISIGSLG+EIF RT+ISNGFAK+YS Sbjct: 182 NHEEIKALAEVVVDHNLWVVSDEIYEKILYDGTEHISIGSLGEEIFKRTIISNGFAKSYS 241 Query: 241 MTGWRLGYLAGPVDIIKAASSIQGHSTSNVCTFAQYGAIAALE--DSQDCVEEMRQAFAK 298 MTGWR+GYLAGP D+IKA S+IQ HSTSNVCTFAQYGAIAALE DS C+++M AF + Sbjct: 242 MTGWRIGYLAGPGDLIKATSTIQSHSTSNVCTFAQYGAIAALESPDSPQCLQKMLDAFTQ 301 Query: 299 RRQVMLDRLNAIPGLSTAKPDGAFYLFPDISKTGLKSLEFCDALIEEHKVAVIPGIAFGA 358 RRQV+L+R+ +IP LS P GAFY+F DIS+TGL SLEFCD L+ + +VA IPG AFGA Sbjct: 302 RRQVILERIRSIPKLSCPTPMGAFYVFIDISQTGLNSLEFCDGLLNKQQVAAIPGKAFGA 361 Query: 359 DDNIRLSYATDLATIEKGLDRLEKFV 384 D+ IRLSYATDLA+IEKG+DR+EKFV Sbjct: 362 DNCIRLSYATDLASIEKGMDRIEKFV 387 Lambda K H 0.317 0.134 0.381 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: 485 Number of extensions: 13 Number of successful extensions: 2 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: 388 Length of database: 390 Length adjustment: 30 Effective length of query: 358 Effective length of database: 360 Effective search space: 128880 Effective search space used: 128880 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 (21.6 bits) S2: 50 (23.9 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