GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msdB1 in Herbaspirillum seropedicae SmR1

Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate HSERO_RS16725 HSERO_RS16725 ABC transporter permease

Query= uniprot:A3DE72
         (327 letters)



>FitnessBrowser__HerbieS:HSERO_RS16725
          Length = 299

 Score =  129 bits (325), Expect = 7e-35
 Identities = 87/292 (29%), Positives = 142/292 (48%), Gaps = 16/292 (5%)

Query: 27  QNLFAYAMLIPTFVCMMCIHFIPMLQGIYLSLLDLNQLTMTKFLN-APFIGLKNYYEILF 85
           +N+     + P  + ++     P+  GI+L   D      TK      FIGL N+  +  
Sbjct: 9   RNVLGMLFMAPAVILLVVFLTYPLGLGIWLGFTD------TKIGGEGSFIGLDNFTYLAG 62

Query: 86  DEKSLIRRGFWFALRNTAIYTVVVTFATFALGIILAMLVNREFKGRGIVRTALLMPWVVP 145
           D  + +      +L NT  YTV  +   F LG+ LA+L+N+    +   R  +L+PW+VP
Sbjct: 63  DSLAQL------SLFNTVFYTVSASILKFMLGLWLAILLNKNVPLKTFFRAIVLLPWIVP 116

Query: 146 SYVVGMTWGFLWRQDSGLINIILCDILHILPEKPYWLVGSNQIWAIIIPTIWRGLPLSMI 205
           + +  + + +L+     +I+  L  +  I     +     N  W+ +   +WRG+P   I
Sbjct: 117 TALSALAFWWLYDAQFSVISWALHKMGLIDRYIDFLGDPWNARWSTVFANVWRGIPFVAI 176

Query: 206 LMLAGLQSISPDYYEAADIDGANGWQKFWHITLPLLKPILAINVMFSLISNIYSFNIVSM 265
            +LAGLQ+ISP  YEAA IDGA  WQ+F H+TLPLL PI+A+ + FS++     F ++ +
Sbjct: 177 SLLAGLQTISPSLYEAAAIDGATPWQQFRHVTLPLLTPIIAVVMTFSVLFTFTDFQLIYV 236

Query: 266 MFGNGAGIPGEWGDLLMTYIQRNTFQMWRFGPGAAALMIVMFFVLGIVALWY 317
           +   G   P     L+ T   +        G GAA    ++ F+L  +   Y
Sbjct: 237 LTRGG---PLNATHLMATLSFQRAIPGGALGEGAALATYMIPFLLAAIMFSY 285


Lambda     K      H
   0.330    0.145    0.468 

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: 336
Number of extensions: 23
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: 327
Length of database: 299
Length adjustment: 27
Effective length of query: 300
Effective length of database: 272
Effective search space:    81600
Effective search space used:    81600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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