Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate 6938545 Sama_2648 aldehyde dehydrogenase (RefSeq)
Query= reanno::Smeli:SM_b20891 (477 letters) >lcl|FitnessBrowser__SB2B:6938545 Sama_2648 aldehyde dehydrogenase (RefSeq) Length = 498 Score = 292 bits (747), Expect = 2e-83 Identities = 175/448 (39%), Positives = 253/448 (56%), Gaps = 8/448 (1%) Query: 32 EYARASAEDAKAAIAAAKAAFPA--WSRSGILERHAILKKTADEILARKDELGRLLSREE 89 + A DA A+A A+A F + WS ++R ++ + A+ + A DEL L + + Sbjct: 51 QVASCQQADADIAVANARAVFESGVWSLQSPVKRKKVMIRFAELLEAHADELALLETLDM 110 Query: 90 GKTLAEGIGETVRAGQIFEFFAGETL-RLAGEVVPSVRPGIGVEITREPAGVVGIITPWN 148 GK +A V ++GE + ++ E+ P+ IG+ ITREP GVV I PWN Sbjct: 111 GKPIAHSKAVDVAGAARAIRWSGEAIDKIYDELAPTPHNEIGM-ITREPVGVVAAIVPWN 169 Query: 149 FPIAIPAWKLAPALCYGNTIVFKPAELVPGCSWAIVDILHRAGLPKGVLNLVMGKGSVVG 208 FP+ + WKL PAL GN++V KP+E P + + + AGLP GVLN++ G G VG Sbjct: 170 FPMLMACWKLGPALATGNSVVLKPSEKSPLTAIRMAQLAKEAGLPDGVLNVLPGFGHTVG 229 Query: 209 QAMLDSPDVQAITFTGSTATGKRVAVASVEHNRK-YQLEMGGKNPFVVLDDA-DLSVAVE 266 QA+ DV + FTGST K++ V + + N K LE GGK+P +V +DA DL A E Sbjct: 230 QALALHMDVDTLVFTGSTKIAKQLMVYAGQSNMKRVWLEAGGKSPNIVFNDAPDLKAAAE 289 Query: 267 AAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAAMGERIKGLVVDDALKPGTHIGPVVDQS 326 AA ++ F+ G+ CTA SR++V G+ D + + + ++ L P T G VVD+ Sbjct: 290 AAASAIAFNQGEVCTAGSRLLVESGVKDELIKLIVKEMEAWQPGHPLDPATTCGAVVDKQ 349 Query: 327 QLNQDTDYIAIGKQEGAKLAFGGEVISRDTPGFYLQPALFTEATNEMRISREEIFGPVAA 386 QL+ YI G EGAKL GG + +T G Y+ P +F TN+M+I+REEIFGPV + Sbjct: 350 QLDTVLGYIKAGHDEGAKLMCGGSQVLAETGGVYVAPTVFDGVTNQMKIAREEIFGPVMS 409 Query: 387 VIRVKDYDEALAVANDTPFGLSSGIATTSLKHATHFKRNAEAGMVMVNLPTAGVDFHVPF 446 VI DEA+A+ANDT +GL++G+ T+ + A + +GMV +N G D PF Sbjct: 410 VITFDGMDEAVAIANDTIYGLAAGVWTSDISKAHKTAKALRSGMVWINHYDGG-DMTAPF 468 Query: 447 GGRKASSYGPREQGKYAAEFYTNVKTAY 474 GG K S G R++ +A E YT VK + Sbjct: 469 GGYKQSGNG-RDKSLHAFEKYTEVKATW 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: 555 Number of extensions: 27 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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