Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate AZOBR_RS24065 AZOBR_RS24065 aspartate aminotransferase
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__azobra:AZOBR_RS24065 Length = 392 Score = 220 bits (561), Expect = 5e-62 Identities = 136/371 (36%), Positives = 200/371 (53%), Gaps = 18/371 (4%) Query: 37 KREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYTALDGTPELKKAIREKFQRENG 96 K G+ VI+L G+PDFDTP V+ AA A+H G+T YT + G PEL+ A+ R G Sbjct: 28 KGRGEDVIVLSVGDPDFDTPAPVRDAAIAALHAGDTHYTPIPGRPELRAALARDVARRTG 87 Query: 97 LAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPYWTSYSDIVHICEGKPVLIACDA 156 L E + + V GA+ LFNA + ++ GDEV++P P + +Y V V +A DA Sbjct: 88 LPVEPENVIVCAGAQNGLFNATLCLVEAGDEVLVPEPMYLTYEACVRASGATLVPVAPDA 147 Query: 157 SSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADYRPLLEVLLRHPHVWLLVDDM 216 ++ RL L AA+TPRTR + L +P+NP+G SA + + ++ RH +W++ D++ Sbjct: 148 AT-LRLDPAALAAAVTPRTRAIFLATPANPTGIVMSAEELEAVADLARRH-DLWVVADEV 205 Query: 217 YEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWRIGYAGGPRELIKAMAVVQ- 275 Y + +D R PG+ RT+T+N +SK++AMTGWR G+ P L+ M + Sbjct: 206 YASLTFD--RPHIGIATLPGMAERTVTINSLSKSHAMTGWRAGWVVAPAPLVAHMGTLAL 263 Query: 276 SQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVVNGLNAIDGLDCRVPEGAFY 335 P + QAA VA G + R E ++RRRD+ + L ++ GL C PE Sbjct: 264 CMLYGLPGFVQQAALVAVEQGDEAVAAMR-EGYRRRRDIALEALGSVPGLRCLKPE---- 318 Query: 336 TFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSAFG--LSPFFRISYATSEA 393 AG+ V G + T +F L + V+V+ AFG + R+S+A SEA Sbjct: 319 -----AGMFMLVDVRGTGLPT-MEFAWRLFRETGVSVLDAGAFGPAAAGCVRLSFAVSEA 372 Query: 394 ELKEALERIAA 404 EL EA RIAA Sbjct: 373 ELAEACRRIAA 383 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: 396 Number of extensions: 23 Number of successful extensions: 5 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