GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlG in Phyllobacterium brassicacearum STM 196

Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, permease component 1 (characterized)
to candidate WP_106712770.1 CU102_RS19475 carbohydrate ABC transporter permease

Query= reanno::WCS417:GFF2491
         (276 letters)



>NCBI__GCF_003010955.1:WP_106712770.1
          Length = 289

 Score =  201 bits (511), Expect = 2e-56
 Identities = 111/280 (39%), Positives = 167/280 (59%), Gaps = 5/280 (1%)

Query: 2   TLQQSRRLQSLLLGTLAWAIAILI-FFPIFWMVLTSFKTEIDAFATPPQFIFT-PTLENY 59
           T ++SR L   L   L   +A+++  FP++W+   SFK +ID FA PP+++   PTL++Y
Sbjct: 9   THKRSRELFVRLSAYLTILVALVVTLFPVYWIAANSFKFDIDIFAVPPEWLPRHPTLKHY 68

Query: 60  LHINERSNYFSYAWNSVLISFSATALCLLISVPAAYSMA--FYETQRTKGTLLWMLSTKM 117
                +  +  YA NS L++   T + +     A Y++A   Y  Q  K    W+LST+M
Sbjct: 69  DEAFIQRPFLRYALNSFLVAMGTTVVSVGFGTMAGYALARFSYPWQWRKQISFWILSTRM 128

Query: 118 LPPVGVLMPIYLLAKSFGLLDTRIALIIIYTLINLPIVVWMVYTYFKDIPKDILEAARLD 177
           +PP+  ++P+YL    F +L+T+ ALII YT  NLP   WM+ +YF+D+P ++ EAA +D
Sbjct: 129 MPPIVSIIPLYLFFNYFDMLNTKSALIIAYTAFNLPFATWMMKSYFQDLPVELEEAAIVD 188

Query: 178 GATLWQEMVRVLLPIAKGGLASTVLLSLILCWNEAFWSLNLT-SSSAAPLTALIASYSSP 236
           G T W   + V LP+A+ GLA+T +  LI+ WNE   SL +T +  +  L   IA   + 
Sbjct: 189 GDTRWGAFLHVALPLARPGLAATAIFCLIISWNEFLLSLIITLTEQSQTLPIGIAGRVTQ 248

Query: 237 EGLFWAKLSAVSTLACAPILIFGWISQKQLVRGLSFGAVK 276
              +W ++SA   +AC PI+IF +I QK LVRGLS GAVK
Sbjct: 249 YKTYWGEISAAGFMACVPIVIFAFIVQKHLVRGLSLGAVK 288


Lambda     K      H
   0.327    0.138    0.427 

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: 266
Number of extensions: 14
Number of successful extensions: 4
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: 276
Length of database: 289
Length adjustment: 26
Effective length of query: 250
Effective length of database: 263
Effective search space:    65750
Effective search space used:    65750
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: 47 (22.7 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