GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Sinorhizobium meliloti 1021

Align glucose transporter, permease component (characterized)
to candidate SM_b20903 SM_b20903 sugar uptake ABC transporter permease

Query= reanno::Phaeo:GFF3640
         (433 letters)



>FitnessBrowser__Smeli:SM_b20903
          Length = 453

 Score =  461 bits (1186), Expect = e-134
 Identities = 231/424 (54%), Positives = 306/424 (72%), Gaps = 8/424 (1%)

Query: 11  EHSKRGLFQQLELDVRLLGMIGAFVILCIGFNILT----DGRFLTPRNIFNLTIQTVSVA 66
           E+  +  F+  E+D RLLGM+GA +I+ +GF ++T    DG FL PRN++NLT+QT SVA
Sbjct: 30  ENPVKRFFRATEIDTRLLGMVGALIIIWLGFQVMTGGLFDGLFLKPRNLWNLTVQTSSVA 89

Query: 67  IMATGMVFVIVTRHIDLSVGALLATCSAVMAVVQTDVLPDMFGLGLNHPATWIITVAVGL 126
           +MATGMV VIVTR+IDLSVG++L  C  +M V+Q  VLP   GLG  HPATW IT+A G+
Sbjct: 90  VMATGMVLVIVTRNIDLSVGSVLGFCGMIMGVLQAQVLPQYLGLG--HPATWAITLACGI 147

Query: 127 AIGTLIGAFQGWMVGFLTIPAFIVTLGGFLVWRNVAWYLTDGQTIGPLDSTF-LVFGGTS 185
           A+G  IGA  G ++ FL +PAFIVTLGG LVWR   W++T GQT+ P+D+TF L+ GGT 
Sbjct: 148 AVGGAIGALHGSIIAFLNVPAFIVTLGGLLVWRGATWFVTSGQTVAPMDATFRLMGGGTE 207

Query: 186 GTLGTTLSWVVGIVATLLALAALWNSRRAKQGHGFPVKPAWAEAVIAGSIAASILGFVAI 245
           G++G T SW+VG +A +  + A+ NSR+ ++  GFP++P WAE  ++    A +LG VA+
Sbjct: 208 GSIGATASWIVGSLACIAIVGAILNSRKQRKRFGFPLRPVWAEYFLSILGCALVLGAVAV 267

Query: 246 LNAYQIPARRLKRMMEAQGETMPEG-LVVGYGLPISVLILIATAVVMTIIARRTRLGRYI 304
            N Y  P    +R  +A G   P+G L + +G+ I VL+ I   +VMT IA R R GRY+
Sbjct: 268 ANHYYWPVNIARRYADANGIAWPDGGLQISHGIAIPVLVAIVVGIVMTFIATRLRFGRYV 327

Query: 305 FATGGNPDAAELSGINTRLLTVKIFALMGFLCALSAVVASARLANHSNDIGTLDELRVIA 364
           FA GGNP+AAEL+GI TR +TVKIF LMG LCA++A +++ARL   +N  G LDEL  IA
Sbjct: 328 FALGGNPEAAELAGIKTRWVTVKIFTLMGVLCAIAAAISTARLNAATNAQGELDELYTIA 387

Query: 365 AAVIGGTALSGGFGTIYGAILGALIMQSLQSGMAMVGVDAPFQNIVVGTVLVAAVWIDIL 424
           AAVIGGT+L+GG GTI GA++GAL+MQSLQSGM ++G+D PFQ IVVG VLV AVW+D +
Sbjct: 388 AAVIGGTSLAGGVGTIAGAMIGALVMQSLQSGMVLLGIDTPFQRIVVGVVLVTAVWLDTV 447

Query: 425 YRKR 428
           YR R
Sbjct: 448 YRAR 451


Lambda     K      H
   0.327    0.141    0.419 

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: 722
Number of extensions: 41
Number of successful extensions: 5
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: 433
Length of database: 453
Length adjustment: 32
Effective length of query: 401
Effective length of database: 421
Effective search space:   168821
Effective search space used:   168821
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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