GapMind for catabolism of small carbon sources

 

Aligments for a candidate for davD in Pseudomonas stutzeri RCH2

Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate GFF3587 Psest_3654 succinate-semialdehyde dehydrogenase

Query= SwissProt::Q9I6M5
         (483 letters)



>lcl|FitnessBrowser__psRCH2:GFF3587 Psest_3654
           succinate-semialdehyde dehydrogenase
          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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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 paper from 2022 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