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 GFF374 Psest_0375 NAD-dependent aldehyde dehydrogenases

Query= SwissProt::Q9I6M5
         (483 letters)



>FitnessBrowser__psRCH2:GFF374
          Length = 480

 Score =  305 bits (781), Expect = 2e-87
 Identities = 177/480 (36%), Positives = 260/480 (54%), Gaps = 5/480 (1%)

Query: 6   AKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWR 65
           A + R   ++DG WV +D  Q    N     ++IG   +  AA+  +AI AA +A PAW 
Sbjct: 2   ADVQRYDNFIDGQWVGSDRYQA-NTNPSDLSDVIGEYAQADAAQVEQAIAAARRAFPAWA 60

Query: 66  ALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAKR 125
               + RA+ L +    ++  +++L  L+  E+GK L EA GE+A A +  ++F  E  R
Sbjct: 61  TFGIQARADALEKVGLEILARREELGTLLAREEGKTLPEAIGEVARAGNIFKYFAGECLR 120

Query: 126 IYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQT 185
             G+T+   +P   + V ++P+GV   ITPWNFP A+   K  PALA G  +V+KPA   
Sbjct: 121 QAGETLQSVRPGVGVEVTREPLGVIGLITPWNFPIAIPAWKIAPALAFGNCVVIKPADLV 180

Query: 186 PYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAEC 245
           P  A A+AE+  RAG P GVF++V G   EVG  + +   V  ++FTGS  +GR +   C
Sbjct: 181 PGCAWAIAEIISRAGFPAGVFNLVMGKGREVGEAIVNAKDVDAVSFTGSVGVGRGIAQTC 240

Query: 246 AQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAF 305
                KV LE+GG  P IV DDADL+ AVE    S + + GQ C  ++R+ V +G+YD F
Sbjct: 241 VARGAKVQLEMGGKNPQIVLDDADLNVAVELCTQSAFYSTGQRCTASSRIIVTEGIYDRF 300

Query: 306 VDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALG- 364
           V+ +   + K+ +G+ LE GV  GP++    + +   +I     +GA++  GG+    G 
Sbjct: 301 VEAMVERIKKIKVGSALEQGVDVGPVVSEAQLEQDLRYIEIGKQEGARLACGGERVKCGT 360

Query: 365 -GTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDL 423
            G F  PT+ VD   N  +S++E FGP+A V + KD  E +AM+NDTEFGL++      L
Sbjct: 361 EGYFLAPTLFVDSDPNMRISREEIFGPVANVVKVKDYDEALAMANDTEFGLSAGICTTSL 420

Query: 424 ARVFRVAEQLEYGMVGINTGLISNEV-APFGGIKASGLG-REGSKYGIEDYLEIKYLCLG 481
                     + GMV IN      +   PFGG K S  G RE  +Y  E Y  +K   +G
Sbjct: 421 KYANHFKRHAQAGMVMINLPTAGVDYHVPFGGRKGSSYGPREQGRYAQEFYTTVKTTYIG 480


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: 590
Number of extensions: 27
Number of successful extensions: 3
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: 480
Length adjustment: 34
Effective length of query: 449
Effective length of database: 446
Effective search space:   200254
Effective search space used:   200254
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