Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate BPHYT_RS27000 BPHYT_RS27000 aspartate aminotransferase
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__BFirm:BPHYT_RS27000 Length = 392 Score = 202 bits (515), Expect = 1e-56 Identities = 130/383 (33%), Positives = 202/383 (52%), Gaps = 20/383 (5%) Query: 25 EILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYTALDGTPELK 84 EI ++ +A A G+ VI+L G+PDF TP + + A +A+ G+T Y+A+ G ++ Sbjct: 19 EIHRVAQQAEA---RGEDVIVLSVGDPDFATPAPIVERAIEALRGGDTHYSAVSGREPVR 75 Query: 85 KAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPYWTSYSDIVHI 144 AI + R G A + + GA+ +F A + L+ GDEVI+P P + +Y V Sbjct: 76 AAIAAEHTRMTGCAASAANVILTAGAQNGVFAASLCLLEAGDEVIVPEPMYLTYEACVRA 135 Query: 145 CEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADYRPLLEVLL 204 V + DA+ F + + LEAA+T RT+ + +P NP+G AD + + Sbjct: 136 AGATLVTVPVDAARAFHVDCDALEAAVTSRTKAIFFATPCNPTGVVMQRADLERIARLAC 195 Query: 205 RHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWRIGYAGGP 264 RH +W+L D++Y + ++ V+ A L PG+ RT+T+ +SK++AM GWR+G+A GP Sbjct: 196 RH-DLWVLSDEVYAELTFER-EHVSIAAL-PGMAERTVTLGSLSKSHAMAGWRVGWAIGP 252 Query: 265 RELIKAMA-VVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVVNGLNAID 323 ELI+ M + + P I QAA + A+ E E ++RRRD+V L+ + Sbjct: 253 TELIEHMGRLALAMLYGLPGFIQQAA-LTAVQHKARIAAEMREIYRRRRDVVFERLHRVP 311 Query: 324 GLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSAFG--LS 381 GL C +PE AG+ V SG + T DF L V+++ SAFG + Sbjct: 312 GLRCLLPE---------AGMFMMVDVSGTGLDT-VDFTWQLFRARGVSLLDASAFGETAN 361 Query: 382 PFFRISYATSEAELKEALERIAA 404 F R+ + EA L +A ERIAA Sbjct: 362 GFVRLGFVVDEARLIDACERIAA 384 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: 386 Number of extensions: 24 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: 392 Length adjustment: 31 Effective length of query: 379 Effective length of database: 361 Effective search space: 136819 Effective search space used: 136819 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