Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate GFF1405 HP15_1371 aspartate aminotransferase
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__Marino:GFF1405 Length = 394 Score = 386 bits (992), Expect = e-112 Identities = 197/393 (50%), Positives = 270/393 (68%), Gaps = 4/393 (1%) Query: 13 QPASRISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGET 72 Q +SR+ +I S L + +AA ++ G+ +I LGAGEPDFDTP+H+KQAA +AI+ G+T Sbjct: 4 QLSSRVQAIKPSPTLAVTNKAAELRAAGQDIIGLGAGEPDFDTPDHIKQAAIEAINNGQT 63 Query: 73 KYTALDGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPT 132 KYTA+DGTP LKKAI KF+R+NGL YE ++I V++G KQ FN +A+L+PGDE IIP Sbjct: 64 KYTAVDGTPALKKAIIAKFKRDNGLDYEANQILVSSGGKQSFFNLALATLNPGDEAIIPA 123 Query: 133 PYWTSYSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYS 192 PYW SY D+V + EGKPV+I A + F++T E+LE AIT RTR ++NSPSNPSG AY+ Sbjct: 124 PYWVSYPDMVLVAEGKPVIIETGAETRFKITPEQLENAITERTRLFVINSPSNPSGMAYT 183 Query: 193 AADYRPLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYA 252 + + + EVL +HP++ + DDMYE I++ G F P L +RT +NGVSKAY+ Sbjct: 184 LEELQAIGEVLKKHPNIMIATDDMYEPILWTGKPFCNILNATPELYDRTFVLNGVSKAYS 243 Query: 253 MTGWRIGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRR 312 MTGWRIGYA GP ++I AM +QSQ+TS P+SISQAA+ AAL+G Q + E ++F+ R Sbjct: 244 MTGWRIGYAAGPAKIIGAMKKIQSQSTSNPASISQAAAQAALDGDQGCVGEMVKAFKERH 303 Query: 313 DLVVNGLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAV 372 D +V LN + G++C +G FY F G + + + TD +F LL DA VA+ Sbjct: 304 DWLVEALNKLPGVECLNGDGTFYVFPSFQGAI----DADSSVSTDVEFAEKLLTDAGVAL 359 Query: 373 VPGSAFGLSPFFRISYATSEAELKEALERIAAA 405 VPGSAFG R+S+ATS L++A+ER+ A Sbjct: 360 VPGSAFGCPGHMRLSFATSMENLEKAVERLQKA 392 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: 494 Number of extensions: 22 Number of successful extensions: 2 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