GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglC in Skermanella stibiiresistens SB22

Align glucose transporter, permease component (characterized)
to candidate WP_037456328.1 N825_RS20585 sugar ABC transporter permease

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



>NCBI__GCF_000576635.1:WP_037456328.1
          Length = 410

 Score =  397 bits (1019), Expect = e-115
 Identities = 209/415 (50%), Positives = 276/415 (66%), Gaps = 24/415 (5%)

Query: 15  RGLFQQLELDVRLLGMIGAFVILCIGFNILTDGRFLTPRNIFNLTIQTVSVAIMATGMVF 74
           R L   LE+D RLL M  A V++ +G +ILT G FLT RN++NL++QT  V IMATGMV 
Sbjct: 17  RDLIAALEIDTRLLAMAAALVVIWVGLDILTGGIFLTARNLWNLSVQTSVVGIMATGMVL 76

Query: 75  VIVTRHIDLSVGALLATCSAVMAVVQTDVLPDMFGLGLNHPATWIITVAVGLAIGTLIGA 134
           VIV RHIDLSVG+LL     +MAV+Q ++LP      +    TW++++A GL  G LIGA
Sbjct: 77  VIVARHIDLSVGSLLGFVGMIMAVLQVEILP------IGTSWTWLVSLAAGLIAGCLIGA 130

Query: 135 FQGWMVGFLTIPAFIVTLGGFLVWRNVAWYLTDGQTIGPLDSTF-LVFGGTSGTLGTTLS 193
           FQGW V +  +PAFIVTLGG L++R +AW++T G+T+ P+D TF L+ GG  G++G   S
Sbjct: 131 FQGWWVAYRAVPAFIVTLGGLLIFRGLAWWITQGRTVAPMDPTFQLMGGGLDGSIGAFWS 190

Query: 194 WVVGIVATLLALAALWNSRRAKQGHGFPVKPAWAEAVIAGSIAASILGFVAILNAYQIPA 253
           WVVG V    AL     +R+ +    FPV+P WAEA+I       I+ FV ++N+Y  P 
Sbjct: 191 WVVGAVFIAAALFKTVRTRQRRNRFNFPVRPLWAEALILAVSIGLIVSFVLVMNSYYRPR 250

Query: 254 RRLKRMMEAQGETMPEGLVVGYGLPISVLILIATAVVMTIIARRTRLGRYIFATGGNPDA 313
            ++ +                 G+PI VLILI  AV M+ + + T+ GRY+FA GGNP+A
Sbjct: 251 TQIPQ-----------------GIPIPVLILIVVAVAMSALTKVTKFGRYVFAIGGNPEA 293

Query: 314 AELSGINTRLLTVKIFALMGFLCALSAVVASARLANHSNDIGTLDELRVIAAAVIGGTAL 373
           AEL GIN R +TV IF LMGFL A+S  + +ARL    N  G+L EL VIAAAVIGGT+L
Sbjct: 294 AELGGINVRKVTVMIFVLMGFLAAISGAIQTARLNAGLNSTGSLLELSVIAAAVIGGTSL 353

Query: 374 SGGFGTIYGAILGALIMQSLQSGMAMVGVDAPFQNIVVGTVLVAAVWIDILYRKR 428
           +GG GTI GAILGALIMQSLQSGM ++ +  P Q +V+G VL+ AVW+D +Y+KR
Sbjct: 354 AGGVGTIAGAILGALIMQSLQSGMILLDIATPMQPVVIGLVLIVAVWLDTVYQKR 408


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: 651
Number of extensions: 40
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: 410
Length adjustment: 32
Effective length of query: 401
Effective length of database: 378
Effective search space:   151578
Effective search space used:   151578
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: 50 (23.9 bits)

This GapMind analysis is from Sep 24 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