GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecD in Rhizobium etli CFN 42

Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate WP_042119995.1 RHE_RS27835 iron chelate uptake ABC transporter family permease subunit

Query= CharProtDB::CH_004160
         (318 letters)



>NCBI__GCF_000092045.1:WP_042119995.1
          Length = 346

 Score =  181 bits (460), Expect = 2e-50
 Identities = 112/328 (34%), Positives = 174/328 (53%), Gaps = 13/328 (3%)

Query: 4   ALVIFITLALAGCALLSLHMGVIPVPWRALLT------DWQA---GHEHYYVLMEYRLPR 54
           AL++     +A    +S+ +G +P+P     +       W A      H  V+ +YRL R
Sbjct: 16  ALLLASLCLIAVVVGVSVGIGDLPIPLATTFSAVTNRLGWTAVELNRIHETVIWDYRLSR 75

Query: 55  LLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVLPLL 114
            L+A F GA LA++G ++Q ++RNPLA P +LG++  AS  +V  ++L      + L   
Sbjct: 76  ALVAAFCGAGLALSGAIMQSLLRNPLAEPYVLGISAGASTGAVAIVILGVGAGAVSLSAG 135

Query: 115 AFAGGMAGLILLKMLAKTHQ--PMKLALTGVALSACWASLTDYLMLS--RPQDVNNALLW 170
           AFAG  A    + +L+   +    +  L GVA S  + + T Y++ +    Q   + + W
Sbjct: 136 AFAGAFAAFFFVALLSNGTRGGADRTILAGVAASQLFNASTSYIVTTSANAQQARDVMFW 195

Query: 171 LTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALL 230
           L GS  G  W    +   ++   L   L + R LD  A GD  A++LGV+V   R     
Sbjct: 196 LLGSFSGVRWPEFALVSVVVSFGLAACLLYARVLDAFAFGDEAASSLGVNVSRARMALFA 255

Query: 231 LAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARII 290
           L   MT+T V+  G I F+GLVVPH+ R + G  H RLLP  A+ GA+ +V+AD+ AR +
Sbjct: 256 LTAMMTATIVSMVGSIGFVGLVVPHVARFVVGPLHIRLLPACAIAGAIFMVLADIAARAL 315

Query: 291 HPPLELPVGVLTAIIGAPWFVWLLVRMR 318
            P   LP+GV+TA++G P+F  +L R +
Sbjct: 316 IPNQILPIGVVTALVGVPFFSIILYRFQ 343


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: 250
Number of extensions: 8
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: 346
Length adjustment: 28
Effective length of query: 290
Effective length of database: 318
Effective search space:    92220
Effective search space used:    92220
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 Apr 09 2024. 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