Align Aspartate aminotransferase; AAT; AspAT; EC 2.6.1.1 (characterized)
to candidate WP_037575239.1 BS73_RS22570 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q82DR2 (408 letters) >NCBI__GCF_000744815.1:WP_037575239.1 Length = 415 Score = 697 bits (1799), Expect = 0.0 Identities = 350/415 (84%), Positives = 382/415 (92%), Gaps = 7/415 (1%) Query: 1 MSAATP-------PTERRVSARVGAISESATLAVDAKAKALKAAGRPVIGFGAGEPDFPT 53 MSAA P P +RRVSARVGAI+ESATLAVDAKAKALKAAGRPVIGFGAGEPDFPT Sbjct: 1 MSAAAPTPDPSVRPADRRVSARVGAIAESATLAVDAKAKALKAAGRPVIGFGAGEPDFPT 60 Query: 54 PDYIVQAAIEACSNPKYHRYTPAGGLPELKAAIAAKTLRDSGYEVDASQVLVTNGGKQAI 113 P+YIVQAA+EAC++PK HRYTPAGGLPELK AIA KTLRDSGY V+ +QVLVTNGGKQAI Sbjct: 61 PEYIVQAAVEACTDPKNHRYTPAGGLPELKQAIADKTLRDSGYRVEPAQVLVTNGGKQAI 120 Query: 114 YEAFAAILDPGDEVIVPAPYWTTYPESIRLAGGVPVDVVADETTGYRVSVEQLEAARTEN 173 YEAFAAILD GDEVIVPAPYWTTYPESIRLAGGVPVDVVADETTGY+V+VEQLEAARTEN Sbjct: 121 YEAFAAILDEGDEVIVPAPYWTTYPESIRLAGGVPVDVVADETTGYKVTVEQLEAARTEN 180 Query: 174 TKVLLFVSPSNPTGAVYTREQIEEIGRWAAEKGLWVLTDEIYEHLVYGDAEFHSLPVVVP 233 TKV+LFVSPSNPTG+VYT ++ IG+WAAE GLWVLTDEIYEHLVYGDA+F SLPV+VP Sbjct: 181 TKVVLFVSPSNPTGSVYTEDEARAIGQWAAEHGLWVLTDEIYEHLVYGDAKFTSLPVLVP 240 Query: 234 ELADKCIVVNGVAKTYAMTGWRVGWVIGPKDVIKAATNLQSHATSNVSNVAQVAALAAVS 293 ELA+KCIVVNGVAKTYAMTGWRVGWVIGPKDV+KAA NLQSHATSNV+NVAQ AALAAV+ Sbjct: 241 ELAEKCIVVNGVAKTYAMTGWRVGWVIGPKDVVKAAQNLQSHATSNVNNVAQRAALAAVT 300 Query: 294 GDLTAVAEMREAFDRRRKTIVRMLNEIGGVLCPEPEGAFYAYPSVKALLGKEIRGKRPQD 353 GDL+AV EM+ AFDRRR+TIVRMLNEI G +CPEPEGAFYAYPSVK +LGKEIRGKRP+ Sbjct: 301 GDLSAVEEMKTAFDRRRRTIVRMLNEIPGFVCPEPEGAFYAYPSVKGVLGKEIRGKRPRT 360 Query: 354 TVELAALILEEAEVAVVPGEAFGTPGYLRLSYALGDEDLVEGVSRIQKLLSEAKD 408 + ELA +IL+E EVAVVPGEAFGTPGYLRLSYALGD+DLVEGVSRIQKLL+EA D Sbjct: 361 SAELAEVILDEVEVAVVPGEAFGTPGYLRLSYALGDDDLVEGVSRIQKLLAEATD 415 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: 639 Number of extensions: 19 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: 415 Length adjustment: 31 Effective length of query: 377 Effective length of database: 384 Effective search space: 144768 Effective search space used: 144768 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 Jul 26 2024. The underlying query database was built on Jul 25 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