GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlF in Phaeobacter inhibens BS107

Align MtlF, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate GFF726 PGA1_c07410 binding protein dependent transport system permease

Query= TCDB::O30492
         (296 letters)



>FitnessBrowser__Phaeo:GFF726
          Length = 315

 Score =  114 bits (285), Expect = 3e-30
 Identities = 83/274 (30%), Positives = 139/274 (50%), Gaps = 10/274 (3%)

Query: 6   KNRLANPGWFLVTPSVALLLLWMIVPLGMTLYFSLIRYNLLYPGENQFVGLENFTYFITD 65
           +NR A   W  + P V   L ++I P+  +   S  R++ L  G+ QF+G+EN+   + D
Sbjct: 26  RNRQALAPWLFLAPGVIFFLFYVIFPILQSFNLSFYRWDGL--GDPQFIGMENYRELMDD 83

Query: 66  SGFLPGATNTLLLVGSVLLISVVFGVLISALLEASEFLGRGIVRVLLISPFFIMPTVGAL 125
             F     N L  +  + L+++  G+ I+  L  +   G  + + L   PF I   V  L
Sbjct: 84  RAFEVSLWNNLKWL-LLYLLAIPAGLFIALFLNQT-VTGIRLYKSLFFFPFVISQVVVGL 141

Query: 126 IWKNLIFHPVSGILAAVWKFFGAEPVDWLAHYPLLSIIIIVS--WQWLPFAILLLMTAMQ 183
           ++ +  + P  G+L  V  + G  P++ L    L++  II++  W    + ++L +T + 
Sbjct: 142 VF-SWFYDPTFGLLNQVLAWVGLGPINVLGDPTLVTYGIIIAGLWPQTAYCMILYLTGLN 200

Query: 184 SLDQEQKEAARLDGAGAIAIFWHLTLPHLARPIAVVVMIETIF-LLSVFAEIFTTTNGGP 242
           ++D EQ EAARLDGA    + W++ +P L RP   V  + TI   L  F  I   TNGGP
Sbjct: 201 AVDPEQVEAARLDGAKGAKMLWYVIIPQL-RPATFVAFVVTIIGALRSFDLISIMTNGGP 259

Query: 243 GYASTNLAYLIYNQALVQFDVGMASAGGLIAVVI 276
             +S  L++ ++ +AL ++   M   G  IAVV+
Sbjct: 260 FGSSRVLSFYMFEKALSEYGFRM-GYGAAIAVVL 292


Lambda     K      H
   0.328    0.143    0.437 

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: 249
Number of extensions: 17
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: 296
Length of database: 315
Length adjustment: 27
Effective length of query: 269
Effective length of database: 288
Effective search space:    77472
Effective search space used:    77472
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: 48 (23.1 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