Aligments for a candidate for mglC in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Aligments 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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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources