GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecC in Caldicellulosiruptor hydrothermalis 108

Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate WP_013404169.1 CALHY_RS11790 iron ABC transporter permease

Query= SwissProt::P15030
         (332 letters)



>NCBI__GCF_000166355.1:WP_013404169.1
          Length = 358

 Score =  142 bits (357), Expect = 2e-38
 Identities = 102/329 (31%), Positives = 164/329 (49%), Gaps = 16/329 (4%)

Query: 15  VAALIIIFWLSLFCYSAIPVSGADATRALLPGHTPTLPEALVQNLRLPRSLVAVLIGASL 74
           VA L I+  +      +  +S +D  +A L G +      +V ++RL R + A+L G  L
Sbjct: 29  VAILTILLSIYAISSGSSDLSFSDVLKAFL-GKSDERTALIVFDIRLVRVVAAILAGIGL 87

Query: 75  ALAGTLLQTLTHNPMASPSLLGINSGAALAMAL---------TSALSPTPIAGYSLSFIA 125
           A+ G  +Q+L HNP+ASP  LGI+ GAA   A+          S+ +   +     S + 
Sbjct: 88  AIGGAAIQSLFHNPLASPFTLGISQGAAFGAAIGIIVLGGGVASSAASDSVTILHPSRVV 147

Query: 126 AC---GGGVSWLLVMTAGGGFRHTHDRNKLILAGIALSAFCMGLTRITLLLAED-HAYGI 181
           AC   G  +S  +V+      R + +   ++L+G+ALS+     T I    A D     +
Sbjct: 148 ACAFLGSMLSTAVVLALAQIKRFSPEA--VVLSGVALSSLFSAATTIIQYFASDVKIAAL 205

Query: 182 FYWLAGGVSHARWQDVWQLLPVVVTAVPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLV 241
            +W  G +  A W DV  +   V+ A    L  +   N +   +  A +LGVN+ + R  
Sbjct: 206 VFWTFGDIGRATWDDVKIMAVFVILAWLYFLANSWNYNAIASGEDVAKSLGVNVEKARFF 265

Query: 242 INMLVLLLVGACVSVAGPVAFIGLLVPHLARFWAGFDQRNVLPVSMLLGATLMLLADVLA 301
             ++   +    VS  G + FI L+ PH+AR + G DQR +   S L+GA L+LL+D +A
Sbjct: 266 GILVSSFITSVIVSFLGIIGFICLVAPHIARRFIGNDQRFLTLASGLVGAFLLLLSDTVA 325

Query: 302 RALAFPGDLPAGAVLALIGSPCFVWLVRR 330
           R +  P  LP GAV + +G+P F++L+ R
Sbjct: 326 RLIVSPVVLPVGAVTSFLGAPLFMYLLIR 354


Lambda     K      H
   0.327    0.140    0.436 

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: 244
Number of extensions: 14
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: 332
Length of database: 358
Length adjustment: 29
Effective length of query: 303
Effective length of database: 329
Effective search space:    99687
Effective search space used:    99687
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: 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