GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Caulobacter crescentus NA1000

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA

Query= uniprot:Q1MCU3
         (247 letters)



>FitnessBrowser__Caulo:CCNA_01670
          Length = 339

 Score =  110 bits (276), Expect = 3e-29
 Identities = 70/231 (30%), Positives = 121/231 (52%), Gaps = 10/231 (4%)

Query: 12  LQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVVFE 71
           + +  VE  +G   AL  VD+ +  GE+++L+G +G+GK+TL+ TI G      G V+F+
Sbjct: 3   IAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFD 62

Query: 72  GRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLK------HFAEDVEK 125
           G+D+T       A  R+    +   +F  MTV +N+  G  +   K        A  VE+
Sbjct: 63  GQDVTYASA---AARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEE 119

Query: 126 IFTLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEA 185
           +  L   L+    +    LSGG++Q +++ RAL  +P +LLLDEP   L   + K +   
Sbjct: 120 LLKLV-ELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRE 178

Query: 186 IRKLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPE 236
           +R++++A G+T   V  +   AL L+ R  ++ NG++   G+  ++   PE
Sbjct: 179 LRRVHDATGVTTIFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPE 229


Lambda     K      H
   0.320    0.137    0.387 

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: 193
Number of extensions: 13
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: 247
Length of database: 339
Length adjustment: 26
Effective length of query: 221
Effective length of database: 313
Effective search space:    69173
Effective search space used:    69173
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 (21.8 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