GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecD in Nocardiopsis lucentensis DSM 44048

Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate WP_017596976.1 D471_RS0101440 iron ABC transporter permease

Query= CharProtDB::CH_004160
         (318 letters)



>NCBI__GCF_000341125.1:WP_017596976.1
          Length = 356

 Score =  201 bits (510), Expect = 3e-56
 Identities = 117/277 (42%), Positives = 165/277 (59%), Gaps = 13/277 (4%)

Query: 45  YVLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMP 104
           +++   R PR+  A+FVGA LAVAG ++Q +VRNP+A P ILG++   S ASVGA+LLM 
Sbjct: 69  FIVWRLRAPRVFQAVFVGAGLAVAGAVVQALVRNPVADPHILGLS---SGASVGAVLLMT 125

Query: 105 SLP-----VMVLPLLAFAGGMAGLILLKMLAKTH---QPMKLALTGVALSACWASLTDYL 156
           +L       + LPL AFAG +   +L+  +A+T    +P++L L GVA+      +T +L
Sbjct: 126 TLGSAALGALALPLAAFAGALVAGLLVFAVARTRGTLEPLRLILVGVAIGQLLGGVTSFL 185

Query: 157 MLSRPQD--VNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARA 214
           +L +         L WL GSL G  WS   +    ++    L  +    L++L LG   A
Sbjct: 186 VLRKQSGDAQQQVLFWLLGSLSGARWSSALVCAAAVLALSALLTARAGSLNVLVLGSEGA 245

Query: 215 TTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSAL 274
            +LGV    +R      A  +T T VA  G I F+GLVVP++ R + G  HRR+LPV AL
Sbjct: 246 ASLGVDADRSRERLFAAAALLTGTTVAVAGAIGFVGLVVPNLARLLVGADHRRVLPVCAL 305

Query: 275 TGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFV 311
           +GAL+LV ADL AR +  P ELP+GVLTA++G P+FV
Sbjct: 306 SGALMLVWADLAARTVLRPTELPIGVLTAVVGVPFFV 342


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: 281
Number of extensions: 15
Number of successful extensions: 4
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: 356
Length adjustment: 28
Effective length of query: 290
Effective length of database: 328
Effective search space:    95120
Effective search space used:    95120
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