GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Caulobacter crescentus NA1000

Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate CCNA_00857 CCNA_00857 glucose/fructose transport protein

Query= TCDB::P15729
         (468 letters)



>FitnessBrowser__Caulo:CCNA_00857
          Length = 478

 Score =  452 bits (1162), Expect = e-131
 Identities = 233/458 (50%), Positives = 315/458 (68%), Gaps = 4/458 (0%)

Query: 13  NVKFVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSVSLALLGSALGAF 72
           N+ FV  I  VA +GGF+FG+D+ VING    L+  F    L TGL+V   L+G A+GAF
Sbjct: 21  NMTFVAAIVAVATIGGFMFGYDSGVINGTQEGLESAFNLSKLGTGLNVGAILIGCAIGAF 80

Query: 73  GAGPIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVIAPAYI 132
            AG +AD  GR   MI++A+LF +S+IG+G   +   FI +R++GG+GVGAASV+ P YI
Sbjct: 81  AAGRLADVWGRRTVMIISALLFVISAIGTGAAESSIVFIIFRLIGGLGVGAASVLCPVYI 140

Query: 133 AEVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNPWLFGAAAWRWMFWTE 192
           +EV+PA++RGRL S+QQ+ I++G+  A ++N+ +A  AG S    WL G  AWRWMFW +
Sbjct: 141 SEVTPANIRGRLSSVQQIMIITGLTGAFVANYALAHTAGSSTAEFWL-GLPAWRWMFWMQ 199

Query: 193 LIPALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEG-GDVPSRIEEIQATVSLDHKP 251
           +IPA ++ +C   IPESPRYLVA+G+  +A AIL ++ G G    ++EEI+A++S DHKP
Sbjct: 200 IIPAGVFFLCLLGIPESPRYLVAKGKDAQAEAILSRLFGAGQGAKKVEEIRASLSADHKP 259

Query: 252 RFSDLLSRRGGLLPIV-WIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEEKSLLITVIT 310
            FSDLL      L ++ W G+ L+  QQ VGIN++FYY SVLW+SVGFTE+ SL I +++
Sbjct: 260 TFSDLLDPTTKKLRVILWAGLVLAVFQQLVGINIVFYYGSVLWQSVGFTEDDSLKINILS 319

Query: 311 GFINILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGATVVNGQPTLTGAAGI 370
           G ++IL  L+AI  +DK GRKPLLL+GS GM +TLG+L+  F  AT VNG  TL    G+
Sbjct: 320 GTLSILACLLAIGLIDKIGRKPLLLIGSAGMAVTLGVLTWCFSTATTVNGALTLGDQIGL 379

Query: 371 IALVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFIISTTFPPLL 430
            AL+ ANLYV  F  SWGP++WV+LGEMF N++R +AL+V    QWIANF IS +FP L 
Sbjct: 380 TALIAANLYVIFFNLSWGPVMWVMLGEMFPNQMRGSALAVCGFAQWIANFAISVSFPALA 439

Query: 431 DTVGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468
               L   YG YA SA +S F +   V ET+GK LE M
Sbjct: 440 -AASLPMTYGFYALSAVVSFFLVQKLVHETRGKELEAM 476


Lambda     K      H
   0.325    0.140    0.430 

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: 643
Number of extensions: 32
Number of successful extensions: 6
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: 468
Length of database: 478
Length adjustment: 33
Effective length of query: 435
Effective length of database: 445
Effective search space:   193575
Effective search space used:   193575
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: 51 (24.3 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