Align Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_015820919.1 TERTU_RS10425 succinylglutamate-semialdehyde dehydrogenase
Query= reanno::Smeli:SM_b20891 (477 letters) >NCBI__GCF_000023025.1:WP_015820919.1 Length = 480 Score = 231 bits (588), Expect = 5e-65 Identities = 150/469 (31%), Positives = 243/469 (51%), Gaps = 22/469 (4%) Query: 3 LHQNLIAGEWVGGDG--VANINPSNTDDVVGEYARASAEDAKAAIAAAKAAFPAWSRSGI 60 +H I G W G G + +I P+ T + E AS D A+ +A+ AF W + Sbjct: 1 MHSVFIDGLWREGCGEPIRSIEPA-TGKTLWEGHSASTADVFQAVESAQVAFKPWRNMPL 59 Query: 61 LERHAILKKTADEILARKDELGRLLSREEGKTLAEGIGETVRAGQIFEFFAGETLRLAGE 120 ER +++K A+ +L+R+ EL ++SRE GK E + E + + AG Sbjct: 60 TERTSVVKHFAECLLSRQQELAEIISRETGKPHWESLQEVTAMINKVDISISAQQQRAGT 119 Query: 121 VVPSVRPGIGVEITREPAGVVGIITPWNFPIAIPAWKLAPALCYGNTIVFKPAELVPGCS 180 + + +T P GV+ + P+NFP +P + PAL GNT+VFKP+E P + Sbjct: 120 TRDAQ-----LALTHRPHGVMAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSEKTPYTA 174 Query: 181 WAIVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVQAITFTGSTATGKRVAVASVEHN 240 ++I +AGLP GV+NL+ G G+ VG+ ++DS D+ + FTGS ATG ++ A H Sbjct: 175 QRTLEIWAQAGLPAGVINLIQG-GASVGKTLIDS-DINGVLFTGSHATGVKIHRALAGHP 232 Query: 241 R-KYQLEMGGKNPFVVLDDADLSVAVEAAVNSAFFSTGQRCTASSRIIVTEGIHDRFVAA 299 LE+GG NP +V + ++ VA + SAF STGQRCT + R+++ +R + Sbjct: 233 EILLALELGGNNPLIVDEVDNIDVAAWHVIRSAFISTGQRCTCARRLVLIGNTGERVLER 292 Query: 300 MGERIKGLVVDDALKPGTHIGPVVDQSQLNQDTDYIAIGKQEGAKLAFGGEVISRDTPG- 358 + + + L + + GP++D + Q + K + +A GGE I PG Sbjct: 293 VIQWVPKLAIGH-WQDNPFFGPLIDTMAVQQ------VLKIQDKLIAAGGEAILFAQPGE 345 Query: 359 -FYLQPALFTEATNEMRISREEIFGPVAAVIRVKDYDEALAVANDTPFGLSSGIATTSLK 417 ++ P + + +E+FGP+ V R +++ +A+A+ANDT FGL++G+ + + Sbjct: 346 HAFISPGI-VRINGNKTVFDDEVFGPLLQVYRAENFTQAVALANDTRFGLAAGLLSDNKA 404 Query: 418 HATHFKRNAEAGMVMVNLPTAGVDFHVPFGGRKASSYGPREQGKYAAEF 466 H F + AG++ +N PTAG +PFGG S R YAA++ Sbjct: 405 HQHIFLNESNAGVISINQPTAGASSKLPFGG-TGHSGNHRPSALYAADY 452 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: 590 Number of extensions: 30 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: 480 Length adjustment: 34 Effective length of query: 443 Effective length of database: 446 Effective search space: 197578 Effective search space used: 197578 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 24 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