GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Echinicola vietnamensis KMM 6221, DSM 17526

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Echvi_1333 Echvi_1333 ABC-type (unclassified) transport system, ATPase component

Query= uniprot:Q1MCU2
         (292 letters)



>FitnessBrowser__Cola:Echvi_1333
          Length = 243

 Score =  102 bits (254), Expect = 8e-27
 Identities = 79/262 (30%), Positives = 129/262 (49%), Gaps = 33/262 (12%)

Query: 14  LLKVEHLSMKFGGLMAINDFSFEAKRGDITALIGPNGAGKTTVFNCITGFYKPTMGMITF 73
           +L+ E+L   + G   +N+ S E ++G+I  L+GPNGAGKTT F  I G  KP  G +  
Sbjct: 2   ILRGENLIKIYKGRKVVNNISVEVEQGEIVGLLGPNGAGKTTSFYMIVGLIKPNSGKVFL 61

Query: 74  NQKSGKQYLLERLPDFRITKEARVARTFQNIRLFSGLTVLENLL-VAQHNKLMKASGYTI 132
           +++      +  LP +R  K   +    Q   +F  L+V EN++ V +   L KA+    
Sbjct: 62  DKEE-----ITPLPMYRRAK-LGIGYLAQEASVFRKLSVEENIMAVLEMTNLPKAA---- 111

Query: 133 LGLIGVGPYKREAAEAIELARFWLEKADLIDRADDPAGDLPYGAQRRLEIARAMCTGPEL 192
                    ++E  E +      LE+  L     +    L  G +RR EIARA+   P+ 
Sbjct: 112 ---------QKEKMEEL------LEEFSLTHVRKNLGMVLSGGERRRTEIARALAVDPKF 156

Query: 193 LCLDEPAAGLNP---RESATLNALLKSIRAETGTSILLIEHDMSVVMEISDHVVVLEYGQ 249
           + LDEP AG++P    E  T+ A LK+        IL+ +H+++  + I+D   ++  G+
Sbjct: 157 VLLDEPFAGVDPIAVEEIQTIVAKLKN----KNIGILITDHNVNETLSITDRAYLMFEGK 212

Query: 250 KISDGTPDHVKNDPRVIAAYLG 271
            +  GT + +  D +V   YLG
Sbjct: 213 LLKAGTAEELAADEQVRKVYLG 234


Lambda     K      H
   0.318    0.136    0.386 

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: 164
Number of extensions: 11
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: 292
Length of database: 243
Length adjustment: 25
Effective length of query: 267
Effective length of database: 218
Effective search space:    58206
Effective search space used:    58206
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: 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