Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate 5208455 Shew_0967 aldehyde dehydrogenase (RefSeq)
Query= reanno::Smeli:SM_b20891 (477 letters) >FitnessBrowser__PV4:5208455 Length = 498 Score = 276 bits (707), Expect = 9e-79 Identities = 170/477 (35%), Positives = 257/477 (53%), Gaps = 10/477 (2%) Query: 5 QNLIAGEWVGGDGVANINPSNTDD--VVGEYARASAEDAKAAIAAAKAAFPA--WSRSGI 60 Q I GE+ D + + D V+ + A DA A+A A+ F WS+ Sbjct: 22 QAFINGEYCAADSNDTFDCISPIDGRVLTQVASCDLLDANRAVANAREVFERGDWSQLPP 81 Query: 61 LERHAILKKTADEILARKDELGRLLSREEGKTLA-EGIGETVRAGQIFEFFAGETLRLAG 119 ++R ++ + AD + A +DEL L + + GK + G + A + + ++ Sbjct: 82 VKRKQVMIRFADLLEANRDELALLETLDMGKPIRYSGAVDVAGAARALRWSGEAVDKIYD 141 Query: 120 EVVPSVRPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGC 179 E+ P+ IG+ ITREP GVV I PWNFP+ + WKL PAL GN++V KP+E P Sbjct: 142 EIAPTAHNEIGM-ITREPVGVVAAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLT 200 Query: 180 SWAIVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEH 239 + + + AG+PKGVLN++ G G VG+A+ DV + FTGST K++ + + E Sbjct: 201 AIRMAQLAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYAGES 260 Query: 240 NRK-YQLEMGGKNPFVVLDDA-DLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFV 297 N K LE GGK+P +V +DA +L A AA ++ F+ G+ CTA SR++V G+ + + Sbjct: 261 NMKRVWLEAGGKSPNIVFNDAPNLKEAAIAAASAIAFNQGEVCTAGSRLLVESGVKEELI 320 Query: 298 AAMGERIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTP 357 + ++ L P T G VVDQ QL YI G EGA+L GG+ + +T Sbjct: 321 NLIEAEMQAWQPGHPLDPATTCGAVVDQQQLENVLRYIRAGVAEGAQLRQGGQQVLAETG 380 Query: 358 GFYLQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLK 417 G Y+ P +F NEM I++EEIFGPV +VI +EA+ + NDT +GL++G+ T+ + Sbjct: 381 GVYVAPTIFANVKNEMTIAKEEIFGPVLSVITFDGMEEAIRIGNDTIYGLAAGVWTSDIS 440 Query: 418 HATHFKRNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVKTAY 474 A + +GMV +N G D PFGG K S G R++ +A + YT +K + Sbjct: 441 KAHKTAKALRSGMVWINHYDGG-DMTAPFGGYKQSGNG-RDKSLHAFDKYTEIKATW 495 Lambda K H 0.317 0.134 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: 552 Number of extensions: 28 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: 477 Length of database: 498 Length adjustment: 34 Effective length of query: 443 Effective length of database: 464 Effective search space: 205552 Effective search space used: 205552 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