GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecC in Nocardiopsis lucentensis DSM 44048

Align Fe(3+) dicitrate transport system permease protein FecC; Iron(III) dicitrate transport system permease protein FecC (characterized)
to candidate WP_017596976.1 D471_RS0101440 iron ABC transporter permease

Query= SwissProt::P15030
         (332 letters)



>NCBI__GCF_000341125.1:WP_017596976.1
          Length = 356

 Score =  172 bits (437), Expect = 9e-48
 Identities = 113/302 (37%), Positives = 166/302 (54%), Gaps = 12/302 (3%)

Query: 34  VSGADATRALLPGHTPTLPEA---LVQNLRLPRSLVAVLIGASLALAGTLLQTLTHNPMA 90
           ++GAD     +PG+ P +PEA   +V  LR PR   AV +GA LA+AG ++Q L  NP+A
Sbjct: 51  LAGADG----VPGNGP-VPEAEDFIVWRLRAPRVFQAVFVGAGLAVAGAVVQALVRNPVA 105

Query: 91  SPSLLGINSGAAL-AMALTSALSPTPIAGYSLSFIAACGGGVSWLLVMTAGGGFRHTHDR 149
            P +LG++SGA++ A+ L + L    +   +L   A  G  V+ LLV  A    R T + 
Sbjct: 106 DPHILGLSSGASVGAVLLMTTLGSAALGALALPLAAFAGALVAGLLVF-AVARTRGTLEP 164

Query: 150 NKLILAGIALSAFCMGLTRITLLLAE--DHAYGIFYWLAGGVSHARWQDVWQLLPVVVTA 207
            +LIL G+A+     G+T   +L  +  D    + +WL G +S ARW         V+  
Sbjct: 165 LRLILVGVAIGQLLGGVTSFLVLRKQSGDAQQQVLFWLLGSLSGARWSSALVCAAAVLAL 224

Query: 208 VPVVLLLANQLNLLNLSDSTAHTLGVNLTRLRLVINMLVLLLVGACVSVAGPVAFIGLLV 267
             ++   A  LN+L L    A +LGV+  R R  +     LL G  V+VAG + F+GL+V
Sbjct: 225 SALLTARAGSLNVLVLGSEGAASLGVDADRSRERLFAAAALLTGTTVAVAGAIGFVGLVV 284

Query: 268 PHLARFWAGFDQRNVLPVSMLLGATLMLLADVLARALAFPGDLPAGAVLALIGSPCFVWL 327
           P+LAR   G D R VLPV  L GA +++ AD+ AR +  P +LP G + A++G P FV  
Sbjct: 285 PNLARLLVGADHRRVLPVCALSGALMLVWADLAARTVLRPTELPIGVLTAVVGVPFFVAA 344

Query: 328 VR 329
           +R
Sbjct: 345 LR 346


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: 343
Number of extensions: 20
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: 332
Length of database: 356
Length adjustment: 29
Effective length of query: 303
Effective length of database: 327
Effective search space:    99081
Effective search space used:    99081
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 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