Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate 352902 BT3375 aspartate aminotransferase (NCBI ptt file)
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__Btheta:352902 Length = 386 Score = 201 bits (512), Expect = 2e-56 Identities = 112/363 (30%), Positives = 196/363 (53%), Gaps = 15/363 (4%) Query: 43 VIILGAGEPDFDTPEHVKQAASDAIHRGETKYTALDGTPELKKAIREKFQRENGLAYE-L 101 VI G+PD + +K+A AI G T+Y+ G EL++ I +++ + + Y Sbjct: 29 VIDFTLGDPDIHPHDKIKEAGCKAILEGRTRYSPNAGLLELREIISSRYKLQYNIEYNPT 88 Query: 102 DEITVATGAKQILFNAMMASLDPGDEVIIPTPYWTSYSDIVHICEGKPVLIACDASSGFR 161 +EI V G + L+ ++A L+ GDEVIIP PYW +Y +V +C G+P++ A +++ Sbjct: 89 NEIMVTVGGMEGLYLTLLAILNRGDEVIIPAPYWINYVQMVCMCSGEPIITAPVSTNDLS 148 Query: 162 LTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADYRPLLEVLLRHPHVWLLVDDMYEHIV 221 ++ E + AITP+T+ ++LN+PSNPSG S + + ++ + + + ++ D++Y+ ++ Sbjct: 149 ISIENIRKAITPKTKAIILNTPSNPSGRIISDDSIQQIAQIAIENDLI-VITDEVYKTLL 207 Query: 222 YDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWRIGYAGGPRELIKAMAVVQSQATSC 281 YD F + + +K RT+ +N +SK + MTGWR+GY P ELI M + Q +C Sbjct: 208 YDNAHFKSIVTCDK-MKERTVVINSLSKEFCMTGWRLGYIAAPSELISVMTMFQENIAAC 266 Query: 282 PSSISQAASVAALNGPQDFLKERTESFQRRRDLVVNGLNAIDGLDCRVPEGAFYTFSGCA 341 SQ A++ AL + + E F RR++++ + I + P+G FY Sbjct: 267 APLPSQYAAIEALRNSEKYSAGMIEEFTLRRNVLLEEVAKIKTITVDAPQGTFY------ 320 Query: 342 GVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSAFG--LSPFFRISYATSEAELKEAL 399 + + +G + +F LLE VAVVPG +G F RI++ ++KE + Sbjct: 321 -AMLNIKSTGLK---SEEFAYALLEKEQVAVVPGITYGDCCEDFIRIAFTLDIYKIKEGI 376 Query: 400 ERI 402 +R+ Sbjct: 377 QRL 379 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: 363 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: 386 Length adjustment: 31 Effective length of query: 379 Effective length of database: 355 Effective search space: 134545 Effective search space used: 134545 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 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