Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate Ga0059261_0516 Ga0059261_0516 vanillin dehydrogenase (EC 1.2.1.67)
Query= reanno::Smeli:SM_b20891 (477 letters) >FitnessBrowser__Korea:Ga0059261_0516 Length = 478 Score = 257 bits (656), Expect = 7e-73 Identities = 165/461 (35%), Positives = 239/461 (51%), Gaps = 9/461 (1%) Query: 15 GDGVANINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGILERHAILKKTADEI 74 G A +NP T +V E + + A A+ AA AAFPAWS G R A L K A+ + Sbjct: 10 GKTFARLNPV-TGEVATEAQAFTVDQANEAVEAAAAAFPAWSTLGPNARRAALNKAAEAL 68 Query: 75 LARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAGEVVPSVRPGIGVEIT 134 A+ ++ ++ E G T + A + A T ++ GEV+PS +PG Sbjct: 69 AAKAEDFVEAMNGEIGATEGWARFNLMLAVSMVREAAALTTQIGGEVIPSDKPGCIAMAI 128 Query: 135 REPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCSWAIVDILHRAGLPK 194 REP GV+ I PWN PI + +A L GNT+V K +E P I + A LPK Sbjct: 129 REPVGVMLGIAPWNAPIILGVRAVAAPLACGNTVVLKASEQCPRTHSLIAEAFDEA-LPK 187 Query: 195 GVLNLVMGKGS----VVGQAMLDSPDVQAITFTGSTATGKRVAVASVEHNRKYQLEMGGK 250 G +++V +VG A++D+P ++ I FTGSTA G+ +A + EH + LE+GGK Sbjct: 188 GAVSIVTNAPEDAPEIVG-ALIDNPHIRRINFTGSTAVGRIIAKRAAEHLKPVLLELGGK 246 Query: 251 NPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAAMGERIKGLVVD 310 P +VL+DADL AV+AA AF + GQ C ++ RIIV + + D FV ++ + V Sbjct: 247 APMLVLEDADLDEAVKAAAFGAFMNQGQICMSTERIIVVDAVADAFVEKFAAKVGTMPVG 306 Query: 311 DALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTPGFYLQPALFTEAT 370 D + T +G VVDQ + I GA GG V+ T G + + T Sbjct: 307 DPREGKTPLGAVVDQKTVAHVKALIGDALAAGAVQVNGGGVL-EGTGGVLMPAHVIDHVT 365 Query: 371 NEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLKHATHFKRNAEAGM 430 +M++ R+E FGPV VIR +D A+ +ANDT +GLS+ + T R ++G+ Sbjct: 366 PDMKLFRDESFGPVVGVIRARDEAHAILLANDTEYGLSASVFTRDTARGLRVARQIKSGI 425 Query: 431 VMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEFYTNVK 471 VN PT + +PFGG KAS YG R GK + +T ++ Sbjct: 426 CHVNGPTVHDEAQMPFGGVKASGYG-RFGGKAGIDAFTELR 465 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: 564 Number of extensions: 31 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: 478 Length adjustment: 34 Effective length of query: 443 Effective length of database: 444 Effective search space: 196692 Effective search space used: 196692 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: 51 (24.3 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