GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__SB2B:6939342 Sama_3435 aldehyde dehydrogenase
           (RefSeq)
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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