GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecD in Halococcus hamelinensis 100A6

Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate WP_007692481.1 C447_RS07405 iron ABC transporter permease

Query= CharProtDB::CH_004160
         (318 letters)



>NCBI__GCF_000336675.1:WP_007692481.1
          Length = 383

 Score =  188 bits (477), Expect = 2e-52
 Identities = 109/300 (36%), Positives = 172/300 (57%), Gaps = 17/300 (5%)

Query: 19  LSLHMGVIPVPWRALLTDWQAGHEHYYVLMEYRLPRLLLALFVGAALAVAGVLIQGIVRN 78
           L L    + +P RAL            ++   RLPR+L+A FVG  LA++G + Q + RN
Sbjct: 88  LGLSTAAVDLPQRAL------------IVWNIRLPRVLVAAFVGTNLAISGAIFQAVTRN 135

Query: 79  PLASPDILGVNHAASLASVGALLLMPSLPVMVLPLLAFAGGMAGLILLKMLAKTH--QPM 136
            LASP ILGV+  A LA +  L++   L  + LP+ A  GG    +++  +A  +   P+
Sbjct: 136 ELASPFILGVSSGAGLAILLTLVVFSGLTAL-LPVTASLGGAVAFLIVYAIAWQNGTSPV 194

Query: 137 KLALTGVALSACWASLTDYLMLSRPQ--DVNNALLWLTGSLWGRDWSFVKIAIPLMILFL 194
           +L L GV +S  + SL   L         V  A+ W TGSL G DW  V+IA+P  IL  
Sbjct: 195 RLVLAGVIVSTVFQSLQTGLFFFADDLGIVQQAISWTTGSLTGTDWEQVRIALPWTILAT 254

Query: 195 PLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVP 254
            L+L+  R L++L LG+  A +LG+SV   RF    +A+   +  ++  G +SF+GL+VP
Sbjct: 255 VLALAGARQLNVLLLGERTAKSLGMSVERVRFALSGIAILAAAASISVAGIVSFVGLIVP 314

Query: 255 HMMRSITGGRHRRLLPVSALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLL 314
           H++R++ G  ++RL+      G  L+V AD+ AR+   P+++PVG++T +IG P+F++L+
Sbjct: 315 HVVRNLVGSDYKRLMVGCVFAGPALMVAADVGARLALNPVQIPVGIVTGLIGGPYFLYLM 374


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: 289
Number of extensions: 9
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: 318
Length of database: 383
Length adjustment: 29
Effective length of query: 289
Effective length of database: 354
Effective search space:   102306
Effective search space used:   102306
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