GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Shewanella loihica PV-4

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate 5211158 Shew_3574 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__PV4:5211158
          Length = 506

 Score =  317 bits (811), Expect = 8e-91
 Identities = 185/483 (38%), Positives = 279/483 (57%), Gaps = 16/483 (3%)

Query: 23  FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82
           FI G++ A    E F+   PV      ++AR    DI+ A+ AA     +  W  +S  +
Sbjct: 22  FIGGQWVAPVGGEYFDNRSPVDGQVFCQVARSDERDIELALDAAHAA--KDAWGKTSVTE 79

Query: 83  RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142
           R  +L K+AD +E + E LA+ ET + GK +R +L  D+P      R++A  I    G  
Sbjct: 80  RSNLLLKIADRVEQNLEFLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQEGSA 139

Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202
           A   ++ ++    EP+GV+  I+PWNFPLL+  WK+ PALAAGN ++LKP+E++P+S + 
Sbjct: 140 ADIDNNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCIVLKPAEQTPVSILV 199

Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262
           +  L ++  LP GVLN+V GFG EAGQAL+    I  +AFTGST+ G  +LK A +S + 
Sbjct: 200 MVELIQDL-LPAGVLNIVNGFGTEAGQALAVSKRIAKLAFTGSTQIGHHILKCAAESLIP 258

Query: 263 RVWLEAGGKSANIVFADCPDLQQAASATAAG----IFYNQGQVCIAGTRLLLEESIADEF 318
              +E GGKS NI FAD  + +      A       F+NQG+VC   +R+L+ ESI D+F
Sbjct: 259 ST-VELGGKSPNIYFADVMEQEDEYLDKAVEGMLLAFFNQGEVCTCPSRVLIAESIYDKF 317

Query: 319 LALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKG-QLLLDGRNAGLAA 377
           +  +  +A+  + G+PLD  T +G        D + S++  G ++G ++L+ G +  L+ 
Sbjct: 318 IDKVIARAKTIKQGNPLDTDTQVGAQASQEQFDKILSYLEIGRNEGAEVLIGGTSCQLSG 377

Query: 378 ------AIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWT 431
                  I PTI    +    + +EEIFGPV+ VT F  E +AL +AND++YGLGA VWT
Sbjct: 378 DQSSGFYIEPTILKGHN-KMRVFQEEIFGPVISVTTFKDEAEALAIANDTEYGLGAGVWT 436

Query: 432 RDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491
           RD++RA RM R ++AG V++N Y+       FGGYK+SG GR+     L  +   K + +
Sbjct: 437 RDMNRAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLSHYQNTKNLLV 496

Query: 492 SLE 494
           S +
Sbjct: 497 SYD 499


Lambda     K      H
   0.317    0.133    0.389 

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: 550
Number of extensions: 24
Number of successful extensions: 6
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: 495
Length of database: 506
Length adjustment: 34
Effective length of query: 461
Effective length of database: 472
Effective search space:   217592
Effective search space used:   217592
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