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) >FitnessBrowser__SB2B:6938545 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 Apr 09 2024. 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