Align Aspartate aminotransferase; AAT; AspAT; Putative 2-aminoadipate transaminase; Transaminase A; EC 2.6.1.1; EC 2.6.1.39 (characterized)
to candidate GFF2092 PGA1_c21250 aspartate aminotransferase AatA
Query= SwissProt::P58350 (410 letters) >FitnessBrowser__Phaeo:GFF2092 Length = 400 Score = 436 bits (1122), Expect = e-127 Identities = 212/392 (54%), Positives = 282/392 (71%) Query: 18 ISSIGVSEILKIGARAAAMKREGKPVIILGAGEPDFDTPEHVKQAASDAIHRGETKYTAL 77 ++ + S + I A ++ G+ VI L AGEPDFDTP+++K+AA AI G+TKYTA Sbjct: 8 LARVKPSPSIAITTLAGELRAAGRDVIGLSAGEPDFDTPDNIKEAAIRAIQAGKTKYTAP 67 Query: 78 DGTPELKKAIREKFQRENGLAYELDEITVATGAKQILFNAMMASLDPGDEVIIPTPYWTS 137 DG ELK+A+ +KF R+NGL Y +++V TG KQIL+NA+MA+L+PGDEV+IP PYW S Sbjct: 68 DGIAELKQAVCDKFARDNGLEYTPAQVSVGTGGKQILYNALMATLNPGDEVVIPAPYWVS 127 Query: 138 YSDIVHICEGKPVLIACDASSGFRLTAEKLEAAITPRTRWVLLNSPSNPSGAAYSAADYR 197 Y D+V + G P+ + +GF++T ++LEAAITP+T+W + NSPSNP+GA Y + + Sbjct: 128 YPDMVRLAGGTPICVESSLETGFKITPDQLEAAITPKTKWFVFNSPSNPTGAGYHPNELK 187 Query: 198 PLLEVLLRHPHVWLLVDDMYEHIVYDGFRFVTPAQLEPGLKNRTLTVNGVSKAYAMTGWR 257 L +VLLRHPHVW++ DDMYEH+V+D F F TPAQ+EP L +RTLT NGVSKAYAMTGWR Sbjct: 188 ALTDVLLRHPHVWVMTDDMYEHLVFDDFTFCTPAQIEPKLYDRTLTCNGVSKAYAMTGWR 247 Query: 258 IGYAGGPRELIKAMAVVQSQATSCPSSISQAASVAALNGPQDFLKERTESFQRRRDLVVN 317 IGYA GP+ LI AM +QSQ+TS P +ISQ A+V ALNG QD++ T F+RRRDLV++ Sbjct: 248 IGYAAGPKPLIDAMRKIQSQSTSNPCTISQWAAVEALNGTQDYILPNTAVFRRRRDLVIS 307 Query: 318 GLNAIDGLDCRVPEGAFYTFSGCAGVLGKVTPSGKRIKTDTDFCAYLLEDAHVAVVPGSA 377 L+ I+G+ C VP+GAFY + AG++G+ + G I D F LLE+A VAVV G+A Sbjct: 308 MLSQIEGVACPVPDGAFYVYPSIAGLIGRTSAGGVAITDDEAFAKALLEEADVAVVHGAA 367 Query: 378 FGLSPFFRISYATSEAELKEALERIAAACDRL 409 +GLSP FRISYA ++ L EA RI C L Sbjct: 368 YGLSPNFRISYAAADETLTEACRRIQVFCAAL 399 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: 535 Number of extensions: 18 Number of successful extensions: 1 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: 400 Length adjustment: 31 Effective length of query: 379 Effective length of database: 369 Effective search space: 139851 Effective search space used: 139851 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