Align 2-aminoadipate transaminase (2.6.1.39) (characterized)
to candidate CA265_RS18530 CA265_RS18530 aspartate aminotransferase family protein
Query= reanno::Putida:PP_4108 (416 letters) >FitnessBrowser__Pedo557:CA265_RS18530 Length = 382 Score = 160 bits (404), Expect = 8e-44 Identities = 119/403 (29%), Positives = 189/403 (46%), Gaps = 39/403 (9%) Query: 13 VHPITLSHGRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAA 72 ++ I ++ + VWD + ++Y+D GG V+++GH NP V + Q ++ Y+ N+ Sbjct: 9 LNDIEITKAAGSNVWDANDQQYLDLYGGHAVISIGHTNPHYVNRLTDQLNKVGFYS-NSV 67 Query: 73 PHGPYLALMEQLSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGR 132 + L E+L + V L NSGAEA ENALK+A G++ +IAF G FHGR Sbjct: 68 KIPLQVQLAEKLGE-VSGKKDFQLFLCNSGAEANENALKLASFYNGRKKVIAFTGAFHGR 126 Query: 133 TLATLNLNGK---VAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVE 189 T + + VAP Q V LP+ + + E+ KA Sbjct: 127 TSLAVAVTDNPKIVAPVNQTEN-----VIFLPF---NNEIALEETFKAQGN--------- 169 Query: 190 DVAAFIFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLG 249 +++A I E +QG GG +F Q +R CDE + I D +Q G+GRTG ++ G Sbjct: 170 EISAVIIEGIQGVGGIKEASKSFLQKIRSLCDEYNAVYIADSVQCGYGRTGSFYSHDYSG 229 Query: 250 IEPDLLLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDE 309 +E D+ +AK + G P+ + + G LG T+ GN ++CAAALA L M + Sbjct: 230 VEADVYTMAKGMGNGFPVAGISIASKFKPW--HGELGTTFGGNHLACAAALAVLEVMEKD 287 Query: 310 NLATWGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVME 369 NL E +++ ++++ + + G G M GIE PA+LA V + Sbjct: 288 NLIKNAEEVGNYLIAELKKFE------QVVEVRGRGLMIGIEL--------PAELAHVKK 333 Query: 370 AARARGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCL 412 + K ++IRLL L + +E L E+ + Sbjct: 334 ELLFTHHIFTGEAKP-NVIRLLPALNLTKAHADEFLAAFEKAV 375 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: 371 Number of extensions: 14 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: 416 Length of database: 382 Length adjustment: 31 Effective length of query: 385 Effective length of database: 351 Effective search space: 135135 Effective search space used: 135135 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 Aug 03 2021. The underlying query database was built on Aug 03 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