GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Caulobacter crescentus NA1000

Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA

Query= TCDB::P21630
         (233 letters)



>FitnessBrowser__Caulo:CCNA_03235
          Length = 381

 Score =  107 bits (266), Expect = 4e-28
 Identities = 70/230 (30%), Positives = 127/230 (55%), Gaps = 7/230 (3%)

Query: 1   MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60
           +++F+ V+  +GK+ A+ +VS+ V +GE   L+G +G GK+TLL  L G      G I  
Sbjct: 14  IITFENVTKRFGKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGRILI 73

Query: 61  EGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTD--KDDYQVQMDKVLE 118
           +G+++  +P +   ++ + +V +   VF  +TV +N+A G    +  K + + ++ + LE
Sbjct: 74  DGQDISNVPPN---KRPVNMVFQSYAVFPHMTVADNVAYGLKVDNVPKAEREARVAEALE 130

Query: 119 LFPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGL-APIIIQQIFEIIE 177
           L  +L     ++   +SGG++Q +A+ RAL+ +P++LLLDEP   L A +  Q   E+  
Sbjct: 131 LV-QLGGLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRTELCT 189

Query: 178 QLRREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVR 227
              + G+T  +V  + ++AL LA R  V+  G +    T + L   P  R
Sbjct: 190 LQEKVGITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSR 239


Lambda     K      H
   0.318    0.136    0.374 

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: 12
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: 233
Length of database: 381
Length adjustment: 26
Effective length of query: 207
Effective length of database: 355
Effective search space:    73485
Effective search space used:    73485
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: 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