Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate 5208455 Shew_0967 aldehyde dehydrogenase (RefSeq)
Query= SwissProt::O34660 (495 letters) >FitnessBrowser__PV4:5208455 Length = 498 Score = 410 bits (1053), Expect = e-119 Identities = 212/475 (44%), Positives = 306/475 (64%), Gaps = 4/475 (0%) Query: 23 YIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVDKAVKAARKAFDQGEWRTMSPAS 82 +I+G++ + S TFD +P G L + D ++AV AR+ F++G+W + P Sbjct: 24 FINGEYCAADSNDTFDCISPIDGRVLTQVASCDLLDANRAVANAREVFERGDWSQLPPVK 83 Query: 83 RSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGDIPLAIEHMRYYAGWCTKITGQT 142 R ++M + ADL+E ++ ELA LETLD GKPI + D+ A +R+ KI + Sbjct: 84 RKQVMIRFADLLEANRDELALLETLDMGKPIRYSGAVDVAGAARALRWSGEAVDKIYDEI 143 Query: 143 IPVSGAYFNYTRHEPVGVVGQIIPWNFPLLMAMWKMGAALATGCTIVLKPAEQTPLSALY 202 P + EPVGVV I+PWNFPLLMA WK+G ALATG ++VLKP+E++PL+A+ Sbjct: 144 APTAHNEIGMITREPVGVVAAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 203 Query: 203 LAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAVDKIAFTGSTEIGKKIMSTAAKS-IK 261 +A+L +AG P GV+N++PG+G G+AL H VD + FTGST+I K++M A +S +K Sbjct: 204 MAQLAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYAGESNMK 263 Query: 262 RVTLELGGKSPNILLPDA-NLKKAIPGALNGVMFNQGQVCCAGSRVFIHKDQYDEVVDEM 320 RV LE GGKSPNI+ DA NLK+A A + + FNQG+VC AGSR+ + +E+++ + Sbjct: 264 RVWLEAGGKSPNIVFNDAPNLKEAAIAAASAIAFNQGEVCTAGSRLLVESGVKEELINLI 323 Query: 321 ASYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQKGKDEGAKAVTGGS--CPFEAGYF 378 + ++ + G L T G +V ++Q E VL YI+ G EGA+ GG G + Sbjct: 324 EAEMQAWQPGHPLDPATTCGAVVDQQQLENVLRYIRAGVAEGAQLRQGGQQVLAETGGVY 383 Query: 379 VAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEVIERANHSEYGLAAGLWTENVKQAH 438 VAPT+FANV++EMTIAKEEIFGPVL+ I ++ ++E I N + YGLAAG+WT ++ +AH Sbjct: 384 VAPTIFANVKNEMTIAKEEIFGPVLSVITFDGMEEAIRIGNDTIYGLAAGVWTSDISKAH 443 Query: 439 YIADRLQAGTVWVNCYNVFDAASPFGGYKQSGLGREMGSYALDNYTEVKSVWVNL 493 A L++G VW+N Y+ D +PFGGYKQSG GR+ +A D YTE+K+ W+ L Sbjct: 444 KTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHAFDKYTEIKATWIAL 498 Lambda K H 0.316 0.133 0.391 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: 657 Number of extensions: 30 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: 495 Length of database: 498 Length adjustment: 34 Effective length of query: 461 Effective length of database: 464 Effective search space: 213904 Effective search space used: 213904 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: 52 (24.6 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