GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fecD in Burkholderia phytofirmans PsJN

Align iron(III) dicitrate transport system permease protein FecD (characterized)
to candidate BPHYT_RS20235 BPHYT_RS20235 iron ABC transporter

Query= CharProtDB::CH_004160
         (318 letters)



>FitnessBrowser__BFirm:BPHYT_RS20235
          Length = 702

 Score =  213 bits (541), Expect = 1e-59
 Identities = 117/285 (41%), Positives = 168/285 (58%), Gaps = 6/285 (2%)

Query: 37  WQAGHEHY----YVLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAA 92
           W A  +H      +L++ RLPRL+ AL  GA LA +GVL+Q IVRNPLA P++LGV   A
Sbjct: 407 WLAAFDHRDELARMLLDLRLPRLICALLAGALLAASGVLMQSIVRNPLAGPEVLGVTQGA 466

Query: 93  SLASVGALLLMPSLPVMVLPLLAFAGGMAGLILLKMLAKTHQ--PMKLALTGVALSACWA 150
            LA++ AL++ P      L   + AGG   L L  +L + H+  P+ +ALTG+ +   W 
Sbjct: 467 GLATLAALVMWPLANHSTLAAASLAGGGITLALTLLLNRRHRYAPLAVALTGIVIGTLWT 526

Query: 151 SLTDYLMLSRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALG 210
           +L+ +L+  +       ++WL G  +GR W  V   +P  +L LP+     R LDLLALG
Sbjct: 527 TLSQWLITQQSVQPARFVVWLVGGTYGRSWGEVTTLLPWCVLALPVFALLARPLDLLALG 586

Query: 211 DARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLP 270
           D +A +LG+ +   R   L +A       VAA GP+ FIGL+ PH+   +    HR  L 
Sbjct: 587 DDQAASLGLPIGVLRPLVLTVATLAACAAVAAVGPVGFIGLMAPHLASMLGARAHRTRLW 646

Query: 271 VSALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFVWLLV 315
           ++A  GAL+LVVAD+ AR +  P E+P GVLTA+IGAP+ + LL+
Sbjct: 647 LAAACGALVLVVADIAARTLLAPREIPAGVLTALIGAPYLLALLI 691



 Score =  157 bits (396), Expect = 9e-43
 Identities = 99/283 (34%), Positives = 145/283 (51%), Gaps = 4/283 (1%)

Query: 30  WRALLTDWQAGHEHYYVLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVN 89
           W A  T   A      +L +  +PR+L AL  G  LAVAG L Q + RNPLASPD+LG+ 
Sbjct: 54  WLAAPTGSDAAQLAGILLFDLSVPRILAALVAGGCLAVAGTLFQSLTRNPLASPDLLGIT 113

Query: 90  HAASLASVGALLLMPSLPVMVLPLLAFAG-GMAGLILLKMLAKTHQPMKLALTGVALSAC 148
             A L  + A+L+     V  +PLL   G G A  +          P++L L G      
Sbjct: 114 GGAQLGLLAAMLVPSLAGVASVPLLFACGLGAAACVAAAAGGWRATPLRLVLAGSVCMLL 173

Query: 149 WASLTDYLMLSRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLA 208
           +++LT  ++    Q +    LW +GSL+    + +KIA   ++L L       R LD LA
Sbjct: 174 FSALTTLILAFFEQSIVGVSLWASGSLYQPGAAGLKIAASWLVLPLIALPFVIRPLDPLA 233

Query: 209 LGDARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRR- 267
           LGD  A   GV V  TR  A+++AV   S  V+  GP+S++GL+ P+++R + G +  R 
Sbjct: 234 LGDDAAAAAGVRVDATRLAAMVVAVGFASVAVSVAGPLSYVGLIAPNLLRQMRGAKASRL 293

Query: 268 --LLPVSALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAP 308
             L+P+SAL G  L++V D   + +     L  GV  A +G P
Sbjct: 294 AALVPLSALVGGALVLVTDSAVQALDLDATLSTGVAIAFVGTP 336


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: 605
Number of extensions: 21
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 318
Length of database: 702
Length adjustment: 33
Effective length of query: 285
Effective length of database: 669
Effective search space:   190665
Effective search space used:   190665
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: 51 (24.3 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