GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Caulobacter crescentus NA1000

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__Caulo:CCNA_01670
          Length = 339

 Score =  188 bits (478), Expect = 2e-52
 Identities = 120/316 (37%), Positives = 172/316 (54%), Gaps = 18/316 (5%)

Query: 4   LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63
           + +  VEK +G    L+ ++L+I  GEL+  +GPSG GK+TLLR IAGLE    G +  D
Sbjct: 3   IAIRSVEKQFGRYPALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFD 62

Query: 64  GTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIA----KKSQAEIDAAVEAAAE 119
           G  V     A R +  VFQ YAL+ HMTV +N++F L +     K S+AEI   VE   +
Sbjct: 63  GQDVTYASAAARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEELLK 122

Query: 120 KLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQL 179
            ++L     R P  LSGGQRQRVA+ R++   P V L DEP   LDA +R + R E+ ++
Sbjct: 123 LVELEGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRELRRV 182

Query: 180 KEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPK 239
            +A   +T ++VTHDQ EA+ LA R+ +L  G I Q+G+P ++++ PE  FV  F+G  +
Sbjct: 183 HDATGVTT-IFVTHDQEEALELADRVAILNNGRIEQIGTPDQVHDAPETAFVCGFVG--E 239

Query: 240 MNLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGGDYVF 299
            N   G++ G G      +T    A+ D          A    VRP D      G + + 
Sbjct: 240 ANRFDGQVSG-GRFKAGALTVPASALKD---------GAATAYVRPHDFALDEAGFEVLI 289

Query: 300 EGKVAITEALGEVTLL 315
           E +  +  AL  VT L
Sbjct: 290 E-RAQVQGALTAVTAL 304


Lambda     K      H
   0.316    0.135    0.379 

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: 333
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: 373
Length of database: 339
Length adjustment: 29
Effective length of query: 344
Effective length of database: 310
Effective search space:   106640
Effective search space used:   106640
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 (21.6 bits)
S2: 49 (23.5 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