Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate 353246 BT3720 putative aspartate aminotransferase (NCBI ptt file)
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__Btheta:353246 Length = 383 Score = 184 bits (468), Expect = 3e-51 Identities = 119/387 (30%), Positives = 194/387 (50%), Gaps = 26/387 (6%) Query: 26 ILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYTALDGTPELKK 85 ++ + RA ++++G VI L GEPDFD P V +AA A R T YT G PEL++ Sbjct: 16 VMDVLERANELQKQGVDVIHLEVGEPDFDVPACVAEAAKAAYDRHLTHYTHSLGDPELRR 75 Query: 86 AIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPYWTSYSDIVHIC 145 I +QRE G+ + D I V +G+ + +M + EVI+ P + Y + V Sbjct: 76 EIAAFYQREYGVTVDPDCIVVTSGSSPSILLVLMLLCNSDSEVILSNPGYACYRNFVLAA 135 Query: 146 EGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADYRPLLEVLLR 205 + KPVL+ +G + E + +TP T + +NSP NP+G + R + + Sbjct: 136 QAKPVLVPLSEENGLQYDIEAIRKCVTPHTAGIFINSPMNPTGMLLDESFLRSVASL--- 192 Query: 206 HPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWRIGYAGGPR 265 V ++ D++Y +VY+G A ++ +NG SK +AMTG R+GY P+ Sbjct: 193 --GVPIISDEIYHGLVYEG-----RAHSILEYTDKAFVLNGFSKRFAMTGLRLGYLIAPK 245 Query: 266 ELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVVNGLNAIDGL 325 ++++ +Q C SSI+Q A +AAL ++ + + RR +++ L + G Sbjct: 246 SCMRSLQKLQQNLFICASSIAQQAGIAALRQADSDVERMKQIYDERRRYMISRLREM-GF 304 Query: 326 DCRV-PEGAFYTFSGCAGVLGKVTPSGKRIKTDT-DFCAYLLEDAHVAVVPGSAFGL--S 381 + +V P+GAFY F+ ++ TD+ F +LE+AHV + PG FG Sbjct: 305 EIKVEPQGAFYIFA-----------DARKFTTDSYRFAFDVLENAHVGITPGIDFGTGGE 353 Query: 382 PFFRISYATSEAELKEALERIAAACDR 408 + R SYA S ++E L+RI+ R Sbjct: 354 GYVRFSYANSLESIREGLDRISQYLSR 380 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: 370 Number of extensions: 21 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: 383 Length adjustment: 31 Effective length of query: 379 Effective length of database: 352 Effective search space: 133408 Effective search space used: 133408 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