Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate GFF3587 Psest_3654 succinate-semialdehyde dehydrogenase
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__psRCH2:GFF3587 Length = 488 Score = 739 bits (1907), Expect = 0.0 Identities = 360/486 (74%), Positives = 417/486 (85%), Gaps = 3/486 (0%) Query: 1 MQLKDAKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKA 60 +QL L RQ AY++G W +AD+G ++ NPATGE+IG+VP MG ETRRAIEAA A Sbjct: 3 LQLGQPDLLRQTAYLNGEWCEADSGARTEIFNPATGELIGAVPNMGRGETRRAIEAAQAA 62 Query: 61 LPAWRALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFG 120 PAWRALTAKERA +LRRW++LM+ENQ+DLAR+MT EQGKPLAEA+GE+AYAASFLEWF Sbjct: 63 QPAWRALTAKERAARLRRWYELMLENQEDLARIMTAEQGKPLAEARGEVAYAASFLEWFA 122 Query: 121 EEAKRIYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLK 180 EE KR+YGD IP H DKRI+V K+P+GVTAAITPWNFPSAMITRKAGPALAAGC MVLK Sbjct: 123 EEGKRLYGDVIPAHAGDKRILVQKEPVGVTAAITPWNFPSAMITRKAGPALAAGCAMVLK 182 Query: 181 PASQTPYSALALAELAERAGIPKGVFSVVTGSAG---EVGGELTSNPIVRKLTFTGSTEI 237 PA QTP+SALALA LAERAGIP G+ SV+T A EVG EL NPIVRKL+FTGST + Sbjct: 183 PAPQTPFSALALAALAERAGIPAGLLSVITADAATSREVGAELCENPIVRKLSFTGSTAV 242 Query: 238 GRQLMAECAQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYV 297 G +LM +CA +KK+SLELGGNAPFIVFDDADLDAAVEGA+ISKYRN GQTCVCANR+YV Sbjct: 243 GIKLMQQCAPTLKKLSLELGGNAPFIVFDDADLDAAVEGAMISKYRNAGQTCVCANRIYV 302 Query: 298 QDGVYDAFVDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSG 357 QDG+YDAFVDKL AAVA+L +GNG E GVTTGPLIDA AVAKV+ H+ DA+ KGA +++G Sbjct: 303 QDGIYDAFVDKLSAAVARLKVGNGAEEGVTTGPLIDAAAVAKVQRHLQDALDKGATLLAG 362 Query: 358 GKPHALGGTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASY 417 GKPHALGG FFEPT++ V V+++ETFGPLAP+FRF+DE EVI +NDTEFGLA+Y Sbjct: 363 GKPHALGGNFFEPTLVGGVTSEMAVAREETFGPLAPLFRFRDEDEVIRQANDTEFGLAAY 422 Query: 418 FYARDLARVFRVAEQLEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKY 477 FYARDL+RVFRVAE LEYGMVGINTG+IS EVAPFGG+KASGLGREGSKYG+++Y+EIKY Sbjct: 423 FYARDLSRVFRVAEALEYGMVGINTGVISTEVAPFGGMKASGLGREGSKYGLDEYVEIKY 482 Query: 478 LCLGGI 483 LCLGGI Sbjct: 483 LCLGGI 488 Lambda K H 0.317 0.135 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: 764 Number of extensions: 16 Number of successful extensions: 2 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: 483 Length of database: 488 Length adjustment: 34 Effective length of query: 449 Effective length of database: 454 Effective search space: 203846 Effective search space used: 203846 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