Align Aspartate aminotransferase; AAT; AspAT; EC 2.6.1.1 (characterized)
to candidate WP_026127587.1 D471_RS0110175 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q82DR2 (408 letters) >NCBI__GCF_000341125.1:WP_026127587.1 Length = 402 Score = 660 bits (1702), Expect = 0.0 Identities = 327/400 (81%), Positives = 361/400 (90%), Gaps = 1/400 (0%) Query: 8 TER-RVSARVGAISESATLAVDAKAKALKAAGRPVIGFGAGEPDFPTPDYIVQAAIEACS 66 TER RVSAR+ AISESATLAVDAKAKA+KA GRPVIGFGAGEPDFPTPDYIV+AA+EA Sbjct: 2 TERPRVSARISAISESATLAVDAKAKAMKAEGRPVIGFGAGEPDFPTPDYIVEAAVEAAR 61 Query: 67 NPKYHRYTPAGGLPELKAAIAAKTLRDSGYEVDASQVLVTNGGKQAIYEAFAAILDPGDE 126 P++HRYTPAGGLPELK AIA KT RDSGY V+ SQVLVTNGGKQAIYEAFAA+LDPGDE Sbjct: 62 EPRFHRYTPAGGLPELKKAIAEKTARDSGYRVEPSQVLVTNGGKQAIYEAFAALLDPGDE 121 Query: 127 VIVPAPYWTTYPESIRLAGGVPVDVVADETTGYRVSVEQLEAARTENTKVLLFVSPSNPT 186 VIV APYWTTYPESI+LAGGVPV V DE+TGY VEQLEAARTE TK+L+FVSPSNPT Sbjct: 122 VIVVAPYWTTYPESIKLAGGVPVFVTTDESTGYMAGVEQLEAARTERTKILVFVSPSNPT 181 Query: 187 GAVYTREQIEEIGRWAAEKGLWVLTDEIYEHLVYGDAEFHSLPVVVPELADKCIVVNGVA 246 GAVY REQ+ IGRWA E LWVLTDEIY+HLVYGDAEF S+PV VPELAD+ ++VNGVA Sbjct: 182 GAVYPREQVRAIGRWALEHDLWVLTDEIYQHLVYGDAEFASIPVEVPELADRTVIVNGVA 241 Query: 247 KTYAMTGWRVGWVIGPKDVIKAATNLQSHATSNVSNVAQVAALAAVSGDLTAVAEMREAF 306 KTYAMTGWRVGW+IGP+DV+KAA NLQSHATSNV+NV+Q AA+AAVSGDL+AV MRE+F Sbjct: 242 KTYAMTGWRVGWIIGPEDVVKAAGNLQSHATSNVANVSQAAAIAAVSGDLSAVDTMRESF 301 Query: 307 DRRRKTIVRMLNEIGGVLCPEPEGAFYAYPSVKALLGKEIRGKRPQDTVELAALILEEAE 366 DRRR+TIVRMLNEI GV+CPEP+GAFYAYPSVK +LGKEIRG+RP + ELA LILEEAE Sbjct: 302 DRRRRTIVRMLNEIDGVVCPEPQGAFYAYPSVKGVLGKEIRGRRPSTSTELAELILEEAE 361 Query: 367 VAVVPGEAFGTPGYLRLSYALGDEDLVEGVSRIQKLLSEA 406 VAVVPGEAFGTPGYLRLSYAL DEDLVEGVSR+QKLL+EA Sbjct: 362 VAVVPGEAFGTPGYLRLSYALSDEDLVEGVSRVQKLLAEA 401 Lambda K H 0.315 0.132 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: 594 Number of extensions: 22 Number of successful extensions: 1 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: 408 Length of database: 402 Length adjustment: 31 Effective length of query: 377 Effective length of database: 371 Effective search space: 139867 Effective search space used: 139867 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: 42 (22.0 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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