GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Shewanella amazonensis SB2B

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate 6939342 Sama_3435 aldehyde dehydrogenase (RefSeq)

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__SB2B:6939342
          Length = 506

 Score =  311 bits (797), Expect = 3e-89
 Identities = 188/485 (38%), Positives = 271/485 (55%), Gaps = 20/485 (4%)

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

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

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

Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262
           L    ++  LP GVLNVV GFG EAG AL+    I  +AFTGST  G  +LK A + N+ 
Sbjct: 200 LLETIEDL-LPPGVLNVVNGFGAEAGAALATSKRIAKLAFTGSTEVGNHILKCAAE-NLI 257

Query: 263 RVWLEAGGKSANIVFADCPD-----LQQAASATAAGIFYNQGQVCIAGTRLLLEESIADE 317
              +E GGKS NI FAD  +     L +A        F+NQG+VC   +R+L++ESI D 
Sbjct: 258 PSTVELGGKSPNIYFADVMNHEDNYLDKAIEGMLLA-FFNQGEVCTCPSRVLVQESIYDA 316

Query: 318 FLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLL--------D 369
           F+  +  +A+  + G PLD  T +G        D +  ++  G ++G  +L        D
Sbjct: 317 FIEKVIARAKTIRQGSPLDTDTQVGAQASREQYDKILGYLDIGRAEGAKVLMGGEFKLQD 376

Query: 370 GRNAGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAV 429
           G   G    I PTI    +    + +EEIFGPV+ VT F  E +AL +AND+QYGLGA V
Sbjct: 377 GPEKG-GYYIQPTILKGHN-KMRVFQEEIFGPVVSVTTFKDEAEALAIANDTQYGLGAGV 434

Query: 430 WTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTI 489
           WTRD++ A RM R ++AG V++N Y+       FGGYK+SG GR+     L  +   K +
Sbjct: 435 WTRDMNLAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLSHYQNTKNL 494

Query: 490 WISLE 494
            +S +
Sbjct: 495 LVSFD 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: 547
Number of extensions: 22
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