Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate GFF2657 PS417_13545 arginine aminotransferase
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__WCS417:GFF2657 Length = 664 Score = 207 bits (526), Expect = 1e-57 Identities = 131/399 (32%), Positives = 211/399 (52%), Gaps = 25/399 (6%) Query: 12 FQP-ASRISSIGVS--EILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIH 68 F P RI+ GV+ +I +AA+ +G+ +IIL G+PDF TP + AA A+ Sbjct: 3 FSPFVERIAGQGVAAWDIHHAAFQAAS---QGEDIIILSVGDPDFATPSFITDAAVSALR 59 Query: 69 RGETKYTALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEV 128 G+T YT + G P L++AI ++ + A + + GA+ LF + L GDEV Sbjct: 60 EGDTHYTEIPGRPALREAIAARYSKTLARALSAENVITVAGAQNALFVTSLCLLQAGDEV 119 Query: 129 IIPTPYWTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSG 188 ++ P + +Y + V + C SGFRL A+ L AAITPRTR + ++P+NP+G Sbjct: 120 LVLDPMYVTYEATLKASGATLVRVPCSPESGFRLDAQLLGAAITPRTRAIFFSNPNNPTG 179 Query: 189 AAYSAADYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVS 248 + + + + ++ + +W++VD++YE +V+DG + + A L PG+ R + + +S Sbjct: 180 VVLNLQELQAIADLAIAR-DLWVVVDEVYESLVFDG-EYHSLAAL-PGMAERCVVIGSLS 236 Query: 249 KAYAMTGWRIGY-AGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTES 307 K++AMTGWRIG+ P+ + A +V S P + +AA+ A L D + E Sbjct: 237 KSHAMTGWRIGWIIATPQMVAHAETLVLSMLYGLPGFVMEAATAAVL-AHDDVTQGMREI 295 Query: 308 FQRRRDLVVNGLNAIDGLDCRVPEGAFYTFSGCAGV-LGKVTPSGKRIKTDTDFCAYLLE 366 ++RRRDLV+ GL+A G+ + P+ + G LG + DF L Sbjct: 296 YRRRRDLVMAGLSACPGIKVQAPQAGMFVLVDVRGTGLGSL-----------DFAWRLFR 344 Query: 367 DAHVAVVPGSAFG--LSPFFRISYATSEAELKEALERIA 403 +A V+V+ +AFG F R+S+ E L EA +RIA Sbjct: 345 EAGVSVLDAAAFGAPAQGFVRLSFTLGEERLSEACQRIA 383 Lambda K H 0.318 0.134 0.393 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: 602 Number of extensions: 39 Number of successful extensions: 6 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: 410 Length of database: 664 Length adjustment: 35 Effective length of query: 375 Effective length of database: 629 Effective search space: 235875 Effective search space used: 235875 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: 52 (24.6 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