Align 2-aminoadipate transaminase; 2-aminoadipate aminotransferase; L-2AA aminotransferase; EC 2.6.1.39 (characterized)
to candidate NP_661271.1 CT0367 acetylornithine aminotransferase
Query= SwissProt::Q88FI7 (416 letters) >NCBI__GCF_000006985.1:NP_661271.1 Length = 400 Score = 163 bits (412), Expect = 1e-44 Identities = 123/412 (29%), Positives = 193/412 (46%), Gaps = 50/412 (12%) Query: 15 PITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYA--FNAA 72 P+ ++ G+ + ++ G+RY+D + G+GV +G+ + + +AI QA++ H + F Sbjct: 23 PLDIASGKGSFLYTASGERYLDMIAGVGVNAIGYGDKRLEQAITEQASKYIHVSNLFMQK 82 Query: 73 PHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFD 126 P A + ++S+ V + NSG EA E A+K+AR G T K +++ Sbjct: 83 PQFDLAAKLLEISRMSKVFF------CNSGTEAIEAAIKLARRFAARNGDTDKTQVLSLT 136 Query: 127 GGFHGRTLATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVEL 186 FHGRT L+L K P V +TG+ ++ ++R S Sbjct: 137 NCFHGRTYGALSLTAK-----------PKYVDGFEPLVPETGMIDFNDVEDLERKVS--- 182 Query: 187 AVEDVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFP 246 AA E VQGEGG + AF L+ E LI+ DEIQ+G GRTG F++ Sbjct: 183 --NRTAAVFVEFVQGEGGIHKVSEAFIAKLKELAKEHDFLIVADEIQAGCGRTGAFFSYM 240 Query: 247 RLGIEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALAS---- 302 I+PDL+ +AK + GG+PLGA++G +++ G G T+ GNP++CAA LA Sbjct: 241 PFDIQPDLVCVAKPLGGGLPLGAIIGSEKVAEVFTPGSHGTTFGGNPVACAAGLAMIEAI 300 Query: 303 LAQMTDENLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPA 362 LA +N G A E+ G + GV R ++ Sbjct: 301 LADGLMQNALEVGSMMRTAFEKMAEKHAQILEIRQYGLMIGVTVHREAKY---------- 350 Query: 363 QLAKVMEAARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAE 414 +E A RG+L+ + + ++IRLL PL+I E + LD L+ E Sbjct: 351 ----YVEEALKRGVLV--NATSNNVIRLLPPLSISKEEAQLCLDTLDAIFTE 396 Lambda K H 0.320 0.137 0.402 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: 357 Number of extensions: 15 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: 416 Length of database: 400 Length adjustment: 31 Effective length of query: 385 Effective length of database: 369 Effective search space: 142065 Effective search space used: 142065 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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