Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate Ac3H11_3135 Aspartate aminotransferase (EC 2.6.1.1)
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3135 Length = 394 Score = 189 bits (479), Expect = 2e-52 Identities = 129/397 (32%), Positives = 205/397 (51%), Gaps = 23/397 (5%) Query: 15 ASRISSIGVSEILKIG---ARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGE 71 A RI V E+ K AR A RE P+I L GEPDF P V++AA+ A+H G Sbjct: 7 AERIEPFYVMEVAKAAQALAREVAGTRE--PMIFLNIGEPDFTAPPLVQEAAARAVHSGA 64 Query: 72 TKYTALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIP 131 T+YT G L++ I +Q G+ I V GA L A +A ++ GDE+++P Sbjct: 65 TQYTNALGLDALRERISSWYQSRFGVNVPARRIVVTAGASAALQLACLALIESGDEILMP 124 Query: 132 TPYWTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAY 191 P + V EGK VL+ A+ ++L+A+K+ AA +TR VLL SPSNP+G + Sbjct: 125 DPSYPCNRHFVSAAEGKAVLLPTTAAERYQLSADKVRAAWNEKTRGVLLASPSNPTGTSI 184 Query: 192 SAADYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAY 251 + + R + +V+ H + ++D++Y + Y+ T ++ + +++N SK + Sbjct: 185 APDELRRIHDVVRSHDGI-TMIDEIYLGLSYEEEFGHTALAIDDNI----ISINSFSKYF 239 Query: 252 AMTGWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQ--DFLKERTESFQ 309 MTGWR+G+ P ++ + + C S++SQ A++A ++ + R E F+ Sbjct: 240 NMTGWRLGWMVVPEAMVPVVERLAQNLFICASTVSQYAALACFEAESIAEYERRRAE-FK 298 Query: 310 RRRDLVVNGLNAIDGLDCRV-PEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDA 368 RRD + L + GL V P+GAFY ++ C ++ +G DF L+ A Sbjct: 299 ARRDFFIPALEKL-GLAVPVKPDGAFYAWADCTQAAQRLGVTG-----SWDFAFELMRRA 352 Query: 369 HVAVVPGSAFGL---SPFFRISYATSEAELKEALERI 402 H+AV PG FG F R S A S A+L+E++ R+ Sbjct: 353 HIAVTPGRDFGTFDPERFIRFSTANSMAQLEESVARL 389 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: 353 Number of extensions: 12 Number of successful extensions: 4 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: 394 Length adjustment: 31 Effective length of query: 379 Effective length of database: 363 Effective search space: 137577 Effective search space used: 137577 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: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. 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