Align Aldehyde dehydrogenase family 2 member C4; ALDH1a; Protein REDUCED EPIDERMAL FLUORESCENCE 1; EC 1.2.1.3 (characterized)
to candidate 7025957 Shewana3_3105 aldehyde dehydrogenase (acceptor) (RefSeq)
Query= SwissProt::Q56YU0 (501 letters) >FitnessBrowser__ANA3:7025957 Length = 498 Score = 411 bits (1056), Expect = e-119 Identities = 204/478 (42%), Positives = 313/478 (65%), Gaps = 4/478 (0%) Query: 21 KLFINGQFIDAASGKTFETIDPRNGEVIATIAEGDKEDVDLAVNAARYAFDHGPWPRMTG 80 K +ING++ DAA+G TF+ + P +G V+A +A D+ D ++AV AR F+ G W + Sbjct: 22 KAYINGEYRDAAAGSTFDCVSPIDGRVLAKVASCDQMDANIAVANAREVFESGVWSKTAP 81 Query: 81 FERAKLINKFADLIEENIEELAKLDAVDGGKLFQLGKYADIPATAGHFRYNAGAADKIHG 140 +R +++ +FA+L+EEN ELA L+ +D GK + K DI A R++ A DK++ Sbjct: 82 VKRKQVMIRFAELLEENANELALLETLDMGKPIRFSKAVDIAGAARAIRWSGEAVDKLYD 141 Query: 141 ETLKMTRQSLFGYTLKEPIGVVGNIIPWNFPSIMFATKVAPAMAAGCTMVVKPAEQTSLS 200 E L T + G +EP+GVV I+PWNFP +M K+ PA+A G ++++KP+E++ L+ Sbjct: 142 E-LAPTAHNEIGMITREPVGVVAAIVPWNFPLLMACWKLGPALATGNSVILKPSEKSPLT 200 Query: 201 ALFYAHLSKEAGIPDGVLNIVTGFGSTAGAAIASHMDVDKVSFTGSTDVGRKIMQAAAAS 260 A+ A L+ +AGIP GVLN++ G+G T G A+A HMDVD + FTGST + +++M A S Sbjct: 201 AIRIAELAVQAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYAGES 260 Query: 261 NLKKVSLELGGKSPLLIFNDA-DIDKAADLALLGCFYNKGEICVASSRVFVQEGIYDKVV 319 N+K+V LE GGKSP ++FNDA D+ AA A +N+GE+C A SR+ V+ G+ D+++ Sbjct: 261 NMKRVWLEAGGKSPNIVFNDAPDLKAAAVAAAEAIAFNQGEVCTAGSRLLVESGVKDQLI 320 Query: 320 EKLVEKAKDWTVGDPFDSTARQGPQVDKRQFEKILSYIEHGKNEGATLLTGGKAI--GDK 377 E + E+ W G P D G VDK+Q + ILSYI+ G++EGA+L+ GG+ + Sbjct: 321 ELIAEELASWQPGHPLDPATVSGAVVDKQQLDTILSYIKAGQDEGASLVHGGQQVLAETG 380 Query: 378 GYFIQPTIFADVTEDMKIYQDEIFGPVMSLMKFKTVEEGIKCANNTKYGLAAGILSQDID 437 G ++QPTIF+ V MKI +EIFGPV+S+++F +EE I AN+T YGLAAG+ + DI Sbjct: 381 GVYVQPTIFSQVNNKMKIASEEIFGPVLSVIEFNGMEEAIAIANDTIYGLAAGVWTADIS 440 Query: 438 LINTVSRSIKAGIIWVNCYFGFDLDCPYGGYKMSGNCRESGMDALDNYLQTKSVVMPL 495 + ++++++G++W+N Y G D+ P+GGYK SGN R+ M + D Y + K+ + L Sbjct: 441 KAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSMHSFDKYTEIKATWIAL 498 Lambda K H 0.318 0.136 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: 630 Number of extensions: 29 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: 501 Length of database: 498 Length adjustment: 34 Effective length of query: 467 Effective length of database: 464 Effective search space: 216688 Effective search space used: 216688 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: 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