GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecD in Caldicellulosiruptor hydrothermalis 108

Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate WP_013404169.1 CALHY_RS11790 iron ABC transporter permease

Query= CharProtDB::CH_004160
         (318 letters)



>NCBI__GCF_000166355.1:WP_013404169.1
          Length = 358

 Score =  143 bits (361), Expect = 5e-39
 Identities = 101/288 (35%), Positives = 154/288 (53%), Gaps = 18/288 (6%)

Query: 46  VLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASL-ASVGALLL-- 102
           ++ + RL R++ A+  G  LA+ G  IQ +  NPLASP  LG++  A+  A++G ++L  
Sbjct: 68  IVFDIRLVRVVAAILAGIGLAIGGAAIQSLFHNPLASPFTLGISQGAAFGAAIGIIVLGG 127

Query: 103 -----MPSLPVMVLP-----LLAFAGGMAGLILLKMLA--KTHQPMKLALTGVALSACWA 150
                  S  V +L        AF G M    ++  LA  K   P  + L+GVALS+ ++
Sbjct: 128 GVASSAASDSVTILHPSRVVACAFLGSMLSTAVVLALAQIKRFSPEAVVLSGVALSSLFS 187

Query: 151 SLTDYLMLSRPQDVNNALL--WLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLA 208
           + T  +      DV  A L  W  G +    W  VKI    +IL     L+   + + +A
Sbjct: 188 AATTIIQYFA-SDVKIAALVFWTFGDIGRATWDDVKIMAVFVILAWLYFLANSWNYNAIA 246

Query: 209 LGDARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRL 268
            G+  A +LGV+V   RF+ +L++  +TS  V+  G I FI LV PH+ R   G   R L
Sbjct: 247 SGEDVAKSLGVNVEKARFFGILVSSFITSVIVSFLGIIGFICLVAPHIARRFIGNDQRFL 306

Query: 269 LPVSALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVR 316
              S L GA LL+++D +AR+I  P+ LPVG +T+ +GAP F++LL+R
Sbjct: 307 TLASGLVGAFLLLLSDTVARLIVSPVVLPVGAVTSFLGAPLFMYLLIR 354


Lambda     K      H
   0.330    0.142    0.447 

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: 212
Number of extensions: 5
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: 318
Length of database: 358
Length adjustment: 28
Effective length of query: 290
Effective length of database: 330
Effective search space:    95700
Effective search space used:    95700
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: 49 (23.5 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