Align phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized)
to candidate CA265_RS24850 CA265_RS24850 aldehyde dehydrogenase
Query= BRENDA::Q5P171 (474 letters) >FitnessBrowser__Pedo557:CA265_RS24850 Length = 454 Score = 236 bits (601), Expect = 2e-66 Identities = 145/449 (32%), Positives = 225/449 (50%), Gaps = 11/449 (2%) Query: 21 VVNPATGEVFARVQAGDASHVDQAVAAARAAFPGWSRTPDAERKRLMHALGAALEAHMPE 80 ++NPAT E+ ++ + S + A + A P W+ ER ++ LE + + Sbjct: 3 IINPATAEIITSLEEDNLSTLQLKFDALQKAQPQWAGKTLQERIAVITHFSDLLEVEIEK 62 Query: 81 LMELVTKEAGKPLGGLNGVGSGMEVGGA---IAWTHVTADLELPVEVIQDNDDARIEVHR 137 L ++T E GKPL S E+ GA I W A+ L EV+ D + + Sbjct: 63 LASVLTSEVGKPLQQ-----SRNEINGARARIKWMLANAEKYLADEVMTDEPGIKEIIKY 117 Query: 138 KPLGVVGSITPWNWPLMIAIWHVIPALRAGNTVVIKPSGMTPTATIRFVELAN-AILPPG 196 +PLGVV +I+ WN+P ++ + IPAL +GNTV+ KPS I +L A +P Sbjct: 118 EPLGVVCNISAWNYPYLVGVNVFIPALLSGNTVMYKPSEYATLTGIEIEKLLKKAGVPDD 177 Query: 197 VLNIVTGESGVGSAIAKHPDINKIVFTGSTPTGKNIMQNAAGNLKRLTLELGGNDAGIVL 256 V +I G GSA+ + D N FTGS TGK I + A + LELGG D + Sbjct: 178 VFHIAIGAKETGSALL-NMDFNGYFFTGSYKTGKLIYEKVAAKMVPCQLELGGKDPLYIT 236 Query: 257 PDV-DPKAIAPKLFGVGFHNNGQTCACLKRLYVHDSIYEKVCAELARIAKETVVGDGLVE 315 DV D A A F+NNGQ+C ++R+YV + Y+ C K G E Sbjct: 237 DDVTDVAAAAIGTADGAFYNNGQSCCAVERIYVQEKNYDDYCNAFVTEVKSWKTGIPTAE 296 Query: 316 GTELGPVQNKAQLDFVQELVEDARAHGARILSGGKARSGGGFFFEPTVIADAKDGMRVVD 375 G +G + K Q+ ++ V+DA GA++L+GGKA G G++FEPTV+ D + M V+ Sbjct: 297 GVYIGALTRKEQISVLENQVKDALNKGAKLLTGGKAVEGKGYYFEPTVLTDVTNDMLVMQ 356 Query: 376 EEQFGPVLPVIRYSDIEEVIARANNNENGLGGSIWSKDHAKAAELALRLECGTAWVNEHG 435 EE FGP++ +++ D E + + + GL S+++ +A ++ +L+ G+ + N Sbjct: 357 EESFGPIIGIMKVKDDAEALKMMKDTDYGLTASVYTASQERAEKILAQLDAGSGYWNCCD 416 Query: 436 AVQPDAPFGGVKQSGLGVEFGRYGLEEYT 464 V P+ G K SG+G G+ +T Sbjct: 417 RVSAALPWSGRKYSGIGATLSHQGIRAFT 445 Lambda K H 0.317 0.136 0.405 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: 490 Number of extensions: 23 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: 474 Length of database: 454 Length adjustment: 33 Effective length of query: 441 Effective length of database: 421 Effective search space: 185661 Effective search space used: 185661 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 (21.6 bits) S2: 51 (24.3 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