GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1693 in Sinorhizobium meliloti 1021

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate SMc03120 SMc03120 ABC transporter ATP-binding protein

Query= uniprot:A0A165KC86
         (260 letters)



>FitnessBrowser__Smeli:SMc03120
          Length = 262

 Score =  164 bits (415), Expect = 2e-45
 Identities = 96/252 (38%), Positives = 148/252 (58%), Gaps = 10/252 (3%)

Query: 8   VVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTFE 67
           VVL   G+ + FGG  A+ DV + +   +V+ LIGPNGAGKTT FN++T    P  GT  
Sbjct: 14  VVLSARGLRRDFGGFTAVKDVDLDVHHARVHALIGPNGAGKTTVFNLLTKFLQPTHGTIT 73

Query: 68  LAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVG--RHIRTGSGLFGAVFRTK 125
           L G+    TA  +VA+ G+ R+FQ   +F  +T L+NV V   R  R  +  + ++    
Sbjct: 74  LLGEDITRTAPDKVARMGLVRSFQISAVFPHLTVLDNVRVALQRPNRLATQFWKSL---- 129

Query: 126 GFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEPA 185
              +    +  +A++L+  VG+ K A+  A  LSYG +R LEIA  LA +P+++ LDEP 
Sbjct: 130 ---SSLDTLNGKAEQLIRSVGLDKEANAVAADLSYGRKRVLEIATTLALEPKVLLLDEPM 186

Query: 186 AGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEVQ 245
           AGM   +   + E+I  +  + R +L++EH++ +V  LC  VTVL  G+ +AEG+ A V 
Sbjct: 187 AGMGHEDVGMVAEIIREVARE-RAVLMVEHNLSVVATLCHHVTVLQRGEILAEGDYATVS 245

Query: 246 KNEKVIEAYLGT 257
           ++ +V  AY+GT
Sbjct: 246 EDPRVRTAYMGT 257


Lambda     K      H
   0.319    0.137    0.384 

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: 178
Number of extensions: 8
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: 260
Length of database: 262
Length adjustment: 25
Effective length of query: 235
Effective length of database: 237
Effective search space:    55695
Effective search space used:    55695
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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