GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mtlF in Phaeobacter inhibens BS107

Align SmoF, component of Hexitol (glucitol; mannitol) porter (characterized)
to candidate GFF1647 PGA1_c16700 binding protein-dependent transport system, inner membrane component

Query= TCDB::O30832
         (290 letters)



>FitnessBrowser__Phaeo:GFF1647
          Length = 316

 Score =  135 bits (339), Expect = 2e-36
 Identities = 88/276 (31%), Positives = 140/276 (50%), Gaps = 5/276 (1%)

Query: 12  LMISPAVILLFLWMIVPLSMTLYFSFLRYNLLMPGMESFTGWDNYYYFLTDPAFSAALTN 71
           L +SP ++L+   M++PL + + +SF    LL P    + G++NY    +D  F  AL N
Sbjct: 35  LYLSPMILLIGSVMLIPLIVGISYSFQSIELLNPFATGWVGFENYEKLWSDRKFWIALEN 94

Query: 72  TILLVVGVLLITVVGGVLLALLLDQPFWGQGIVRVLVIAPFFVMPTVSALVWKNMFMNPV 131
           T       +      G+ LA+LL+  F+G+ + + LV  P+ V   +SAL W  +F NPV
Sbjct: 95  TFFWTFWSIFFQFFLGLGLAMLLNTQFFGKKLFQALVFLPWAVPTFLSALTWAWLF-NPV 153

Query: 132 NGMFAHIARGLGL--PPFDFLSQAPLASIIGIVA--WQWLPFATLILLTALQSLDREQME 187
            G   H    LG+   P++ L    LA    I A  W  +PF  + LL ALQS+  E  E
Sbjct: 154 IGPIPHWLAALGVLSEPYNILGDPDLAIWGPITANIWFGVPFFAITLLAALQSIPGELYE 213

Query: 188 AAEMDGASALDRFIHITVPHLTRAITVVVLIQTIFLLGVFAEILVTTNGGPGTASTNITY 247
           AAE+DGA+    F  IT+P L   I + V+++TI++      I V T GGP  ++  ++ 
Sbjct: 214 AAEIDGATPWQSFTKITLPFLAPMIAITVMLRTIWIANFADLIFVMTGGGPANSTQILST 273

Query: 248 LVYAQSLLNYDVGGGSAGGIVAVVLANIVAIFLMRM 283
            ++  +    D G  S   +  +++    A+ L+ M
Sbjct: 274 YIFTTAFRKLDFGYASTIAVALLIILLAYAVILLWM 309


Lambda     K      H
   0.329    0.142    0.429 

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: 276
Number of extensions: 19
Number of successful extensions: 2
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: 290
Length of database: 316
Length adjustment: 27
Effective length of query: 263
Effective length of database: 289
Effective search space:    76007
Effective search space used:    76007
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 (21.8 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