GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecD in Paraburkholderia bryophila 376MFSha3.1

Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate H281DRAFT_00137 H281DRAFT_00137 iron complex transport system permease protein

Query= CharProtDB::CH_004160
         (318 letters)



>FitnessBrowser__Burk376:H281DRAFT_00137
          Length = 352

 Score =  174 bits (441), Expect = 3e-48
 Identities = 120/340 (35%), Positives = 181/340 (53%), Gaps = 29/340 (8%)

Query: 2   KIALVIFITLALAGCALL--SLHMGVIPV----------PWRALLTDWQAGHEHYYVLME 49
           K A  I++ LALA  A+L  SL +G + +          P  A  +D  +      ++  
Sbjct: 18  KRAAAIWLVLALAALAVLMASLALGSVSLAPARVIEALSPLHAGASDANSADLAGEIVRT 77

Query: 50  YRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVM 109
            RLPR L     GA LA+AG L+Q ++RNPLA P +LGV+  A  A+   + ++      
Sbjct: 78  LRLPRALAGFACGALLALAGALLQVLLRNPLAEPYVLGVSGGA--ATFALVAMIAGCAWW 135

Query: 110 VLPLLAFAGGMAGLILLKMLAKTH----QPM----KLALTGVALSACWASLTDYLMLSRP 161
           ++   AFAG    ++L+  LA+      +P     +L LTG  ++A W +L   L+   P
Sbjct: 136 LVDASAFAGAFVSILLVLGLARRELWRGEPQDTSPRLLLTGAVIAAGWGALITLLLNLAP 195

Query: 162 QD-VNNALLWLTGSLWGR--DWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLG 218
            + +   L WLTG L G    W+ +   + ++I  +P++      L++L  GDA A  LG
Sbjct: 196 DNRLRGMLFWLTGDLNGNALPWTALVALVVVLIAIVPVAPR----LNVLLRGDAAAQALG 251

Query: 219 VSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGAL 278
           V+V   R    L A    +  V   G I F+GLVVPHM+R   G   R LLP +AL G +
Sbjct: 252 VAVMPLRLRVYLAASLAAAAAVTTAGTIGFVGLVVPHMLRLAFGNDQRMLLPAAALGGGV 311

Query: 279 LLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLVRMR 318
            ++ ADL+AR++  P +LPVGV+T+IIG P F+W+L+R R
Sbjct: 312 AVMGADLIARLVIAPAQLPVGVITSIIGVPVFLWMLLRAR 351


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: 316
Number of extensions: 18
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: 352
Length adjustment: 28
Effective length of query: 290
Effective length of database: 324
Effective search space:    93960
Effective search space used:    93960
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