Alignments for a candidate for mglC in Rhodobacter johrii JA192

GapMind for catabolism of small carbon sources

Alignments for a candidate for mglC in Rhodobacter johrii JA192

Align glucose transporter, permease component (characterized)
to candidate WP_069332197.1 C8J29_RS16905 sugar ABC transporter permease

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



>NCBI__GCF_003046325.1:WP_069332197.1
          Length = 432

 Score =  620 bits (1599), Expect = 0.0
 Identities = 310/430 (72%), Positives = 358/430 (83%), Gaps = 1/430 (0%)

Query: 1   MTETTSQPIPEHSKRGLFQQLELDVRLLGMIGAFVILCIGFNILTDGRFLTPRNIFNLTI 60
           M++T + P     KR   + LE+D RLLGMIGAFV+LC+ F+  TDGRFLTPRNIF L I
Sbjct: 1   MSDTANAPGAAR-KRSFIETLEIDTRLLGMIGAFVVLCLVFHFQTDGRFLTPRNIFTLAI 59

Query: 61  QTVSVAIMATGMVFVIVTRHIDLSVGALLATCSAVMAVVQTDVLPDMFGLGLNHPATWII 120
           QTVSVAIMATGMVFVIVTRHIDLSVG+LLA CSAVM ++Q  VLP M G+    P    +
Sbjct: 60  QTVSVAIMATGMVFVIVTRHIDLSVGSLLALCSAVMGMMQVVVLPQMMGIDFGSPLIAPV 119

Query: 121 TVAVGLAIGTLIGAFQGWMVGFLTIPAFIVTLGGFLVWRNVAWYLTDGQTIGPLDSTFLV 180
            +A GL +G  IGAF GW++G+L IP+FIVTLGG L+WRNVAWYLT GQTIGPLD TF +
Sbjct: 120 AIAAGLVVGVAIGAFNGWLIGYLGIPSFIVTLGGLLIWRNVAWYLTSGQTIGPLDQTFQL 179

Query: 181 FGGTSGTLGTTLSWVVGIVATLLALAALWNSRRAKQGHGFPVKPAWAEAVIAGSIAASIL 240
           FGG +GT+G   SW++G V T  AL  LW++RRAKQ HGF VKP WAE V+ G ++A+IL
Sbjct: 180 FGGINGTIGPFWSWILGGVGTAAALWGLWSARRAKQSHGFAVKPVWAELVMGGVLSAAIL 239

Query: 241 GFVAILNAYQIPARRLKRMMEAQGETMPEGLVVGYGLPISVLILIATAVVMTIIARRTRL 300
           GFVAI+NAY++PA RL+R+ EA+GET+PEG   GYGLPISVL+L+A A+ MT+IA+RTR 
Sbjct: 240 GFVAIVNAYEVPAARLRRLFEARGETLPEGYTTGYGLPISVLLLVAVAIAMTVIAKRTRF 299

Query: 301 GRYIFATGGNPDAAELSGINTRLLTVKIFALMGFLCALSAVVASARLANHSNDIGTLDEL 360
           GRYIFATGGNPDAAELSGINTRLLTVKIFAL+G LCALSAVVASARL NH+NDIGTLDEL
Sbjct: 300 GRYIFATGGNPDAAELSGINTRLLTVKIFALLGGLCALSAVVASARLTNHANDIGTLDEL 359

Query: 361 RVIAAAVIGGTALSGGFGTIYGAILGALIMQSLQSGMAMVGVDAPFQNIVVGTVLVAAVW 420
           RVIAAAVIGGTALSGG GTIYGAILGA+IMQSLQSGMAMVGVDAPFQNIVVG+VLV AV 
Sbjct: 360 RVIAAAVIGGTALSGGMGTIYGAILGAIIMQSLQSGMAMVGVDAPFQNIVVGSVLVLAVL 419

Query: 421 IDILYRKRVG 430
           IDI+YRKR G
Sbjct: 420 IDIIYRKRTG 429


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: 791
Number of extensions: 43
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: 433
Length of database: 432
Length adjustment: 32
Effective length of query: 401
Effective length of database: 400
Effective search space:   160400
Effective search space used:   160400
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 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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