GapMind for catabolism of small carbon sources

 

Alignments 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)



>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.

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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:

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