GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS03645 in Caulobacter crescentus NA1000

Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP

Query= uniprot:D8IZC8
         (344 letters)



>FitnessBrowser__Caulo:CCNA_00904
          Length = 332

 Score =  218 bits (555), Expect = 2e-61
 Identities = 128/306 (41%), Positives = 186/306 (60%), Gaps = 9/306 (2%)

Query: 43  LLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAV 102
           +LF  L + + G     F +A N +NIL +V+I  ++A GMTFVIL  GID++VGS+LA 
Sbjct: 29  ILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILIGGIDVAVGSLLAF 88

Query: 103 SAVLGMQVS---LGAAPG-WAIPMFIFS--GLVMGMVNGAMVALLNINAFVVTLGTMTAF 156
           +++    V    +G  P  W I + + +  GL  G V G  V  L++ AF+VTLG MT +
Sbjct: 89  ASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHVPAFIVTLGGMTVW 148

Query: 157 RGAAYLLADGTTVLN-NDIPSFEWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHI 215
           RGA  LL DG  +   ND  ++ W G+G+ L +P  + +   V     V LR T  G  +
Sbjct: 149 RGATLLLNDGGPISGFND--AYRWWGSGEILFLPVPVVIFALVAAAGHVALRYTRYGRQV 206

Query: 216 YAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIA 275
           YA+GGN +AARL+G+ V  +   VY+I G  +GL+G + ++RL  A    G+GYEL  IA
Sbjct: 207 YAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGSAEAVAGTGYELRVIA 266

Query: 276 AVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDKW 335
           +VV+GG SL GG G + GTV+GAL+IGV++NGL +L ++S+ Q V  G +IV AV  D +
Sbjct: 267 SVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQVVIGLIIVAAVAFDHY 326

Query: 336 RQKDAA 341
            +   A
Sbjct: 327 ARTHKA 332


Lambda     K      H
   0.324    0.138    0.417 

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: 352
Number of extensions: 16
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: 344
Length of database: 332
Length adjustment: 28
Effective length of query: 316
Effective length of database: 304
Effective search space:    96064
Effective search space used:    96064
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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