GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msdB2 in Pseudomonas fluorescens GW456-L13

Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate PfGW456L13_1896 Glucose ABC transport system, inner membrane component 2

Query= uniprot:A3DE71
         (289 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1896
          Length = 281

 Score =  122 bits (305), Expect = 1e-32
 Identities = 83/272 (30%), Positives = 136/272 (50%), Gaps = 12/272 (4%)

Query: 21  ANIILAILVVLTLGPIVFMVLTSLMDHNAIARGKWIA-PTRFSNYVEVFQKLPFGIYFRN 79
           A ++LA  V L   P+V M+LTS      I  G  ++ PT       +      G YF N
Sbjct: 19  ATLLLAAAVYLI--PLVVMLLTSFKSPEDIRTGNLLSWPTVIDGIGWIKAWDVVGGYFWN 76

Query: 80  SLIVCSIVMVVALVIATLAGYSLAKYKFPGSGFFGILILATQLLPGMMFLLPLYLDFVKI 139
           S+ +    ++++  I  + GY L+ ++F GS  F  L+L    LP    LLP      K 
Sbjct: 77  SVKITVPAVLISTFIGAMNGYVLSMWRFRGSQLFFGLLLFGCFLPFQTVLLPASFTLGKF 136

Query: 140 KQATGIQLINSIPGLVIVYSAFFVPFSIWIIRGFFASIPGELEEAARIDGCNKFTAFLRV 199
                  L N+  GLV+V+  + + F+    R ++ SIP  L +AAR+DG   FT FL++
Sbjct: 137 G------LANTTTGLVLVHVVYGLAFTTLFFRNYYVSIPDALVKAARLDGAGFFTIFLKI 190

Query: 200 MLPLAVPGIVATAIYIFLTAWDELIFAWVLLKDTKVTTIPAGIRGFIAYTTA--RYDLLM 257
           +LP+++P ++   I+ F   W++ +F  V+        I   +   +  +T    Y++ M
Sbjct: 191 LLPMSIPIVMVCLIWQFTQIWNDFLFG-VVFASGDAQPITVALNNLVNTSTGAKEYNVDM 249

Query: 258 AAGTIVTIPVLIMFFTMQKKFISGMTAGAVKG 289
           AA  I  +P L+++    K F+ G+T+GAVKG
Sbjct: 250 AAAMIAGLPTLLVYIFAGKYFLRGLTSGAVKG 281


Lambda     K      H
   0.332    0.145    0.434 

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: 264
Number of extensions: 15
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: 289
Length of database: 281
Length adjustment: 26
Effective length of query: 263
Effective length of database: 255
Effective search space:    67065
Effective search space used:    67065
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 47 (22.7 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