Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate 8501474 DvMF_2204 aminotransferase class I and II (RefSeq)
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__Miya:8501474 Length = 390 Score = 303 bits (777), Expect = 4e-87 Identities = 158/389 (40%), Positives = 237/389 (60%), Gaps = 7/389 (1%) Query: 15 ASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKY 74 + R++ I S L + A+A +K +G V+ L GEPDF TPEHV++AA AI +G T+Y Sbjct: 4 SDRLTRIKPSATLAVNAKALELKAKGVQVVSLAVGEPDFPTPEHVREAAKTAIDQGFTRY 63 Query: 75 TALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPY 134 T + G PEL++A+ F R G+ ++ V G KQ L+N L+PGDEV++P PY Sbjct: 64 TQVPGIPELRQAVCGYFARFYGVEAPMEATVVTNGGKQALYNLFQCLLNPGDEVLVPAPY 123 Query: 135 WTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAA 194 W SY +V + G PV +A A GF++T E+L+ A+TP+TR +LLNSPSNP+GA YS A Sbjct: 124 WVSYPALVELAGGVPVFVASPAERGFKVTPEELDRAVTPKTRVLLLNSPSNPTGACYSRA 183 Query: 195 DYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMT 254 + ++E + ++++ D++Y+ +VY+ V+ VNG++K +AMT Sbjct: 184 ETDAIMEWAIAR-DLFVVSDEIYDRLVYEPAEAVSVCDWWERHPENVAVVNGLAKTFAMT 242 Query: 255 GWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDL 314 GWR+GYA +LIKAM +Q Q+TS S++Q A++AAL GP D ++E +SF+RRRDL Sbjct: 243 GWRVGYALAHPDLIKAMTKIQGQSTSNICSVAQKAALAALTGPYDAVEEMKKSFRRRRDL 302 Query: 315 VVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVP 374 +++ G+ C P+GAFY F+ + P C Y++E A+VA+VP Sbjct: 303 AHGIVSSWPGVICPKPDGAFYLFADMRALFTPALPD------SASLCTYIMEQANVALVP 356 Query: 375 GSAFGLSPFFRISYATSEAELKEALERIA 403 G+AFG R SYA S+ L AL+++A Sbjct: 357 GAAFGDDACLRFSYAVSDDTLMIALDKVA 385 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: 417 Number of extensions: 13 Number of successful extensions: 3 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: 390 Length adjustment: 31 Effective length of query: 379 Effective length of database: 359 Effective search space: 136061 Effective search space used: 136061 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