GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecD in Echinicola vietnamensis KMM 6221, DSM 17526

Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate Echvi_3111 Echvi_3111 ABC-type Fe3+-siderophore transport system, permease component

Query= CharProtDB::CH_004160
         (318 letters)



>FitnessBrowser__Cola:Echvi_3111
          Length = 357

 Score =  183 bits (465), Expect = 5e-51
 Identities = 109/290 (37%), Positives = 165/290 (56%), Gaps = 14/290 (4%)

Query: 42  EHYYVLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALL 101
           E   VL   R PR++L + VG +LAVAG  +QG+ RNPL  P I+GV+  ++L +V  ++
Sbjct: 64  EKMAVLWAIRFPRVVLGVLVGGSLAVAGACLQGLFRNPLVEPAIIGVSSGSALFAVIVIV 123

Query: 102 LMPSLP--------VMVLPLLAFAGGMAGLILLKMLA----KTHQPMKLALTGVALSACW 149
              S+            LPL AF GG+    L   LA    KT   + L L GVA++A  
Sbjct: 124 FSSSIGWQLQSVFGAFALPLAAFTGGLLNTFLAYRLASKAGKTDISI-LILAGVAINALS 182

Query: 150 ASLTDYLML-SRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLA 208
           A+L   ++       + N   W  GSL G  WS V I    + L   + LSF R L+ LA
Sbjct: 183 AALIGLVIYYGDDHAIRNFTFWSLGSLGGASWSKVYIVGVFIFLSTVVMLSFPRSLNALA 242

Query: 209 LGDARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRL 268
           +G+A A  +G++V   +   L  +      GV+  G I F+GLVVPH++R + G  HR L
Sbjct: 243 VGEAEAYHMGINVQRVKHLLLFFSALAVGAGVSVTGAIGFVGLVVPHLVRMLLGADHRIL 302

Query: 269 LPVSALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVRMR 318
           LP++ L GA+L++VAD+++R++  P EL +G++TA+IGAP+F+ +L+  +
Sbjct: 303 LPMAFLFGAILMLVADVVSRLVVAPAELSIGIITALIGAPFFISILMNFK 352


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: 269
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: 357
Length adjustment: 28
Effective length of query: 290
Effective length of database: 329
Effective search space:    95410
Effective search space used:    95410
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 17 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