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_04922 H281DRAFT_04922 iron complex transport system permease protein

Query= CharProtDB::CH_004160
         (318 letters)



>FitnessBrowser__Burk376:H281DRAFT_04922
          Length = 663

 Score =  130 bits (327), Expect = 9e-35
 Identities = 94/305 (30%), Positives = 154/305 (50%), Gaps = 23/305 (7%)

Query: 25  VIPVPWRALLTDWQ-AGHEHYYVLMEYRLPRLLLALFVGAALAVAGVLIQGIVRNPLASP 83
           VI + +   +  WQ    +H+  +  +R+PRL  +L  G  +A+AG ++Q +  NP+ASP
Sbjct: 369 VISLCFSVTMQGWQWTDAQHWSDVWFWRVPRLTASLGAGVMVALAGTILQRVTGNPMASP 428

Query: 84  DILGVNHAASLASVGALLLM--PSLPVMVLPLLAFAGGMAGLILLKMLAKTH--QPMKLA 139
           D+LGV+  A L  + A ++   PS PV++    + AG +  L+ +  L +     P  + 
Sbjct: 429 DLLGVSGGAMLGMLVAAVVATEPSTPVLLAG--SAAGALVCLLTIVTLGRRSGFAPEHVL 486

Query: 140 LTGVALSA--------CWASLTDYLMLSRPQDVNNALLWLTGSLWGRDWSFVKIAIPLMI 191
           L G+A+SA          AS   Y  L RP    +  L +  +        + + +  + 
Sbjct: 487 LAGIAISAFAQAVIMLATASGGAYANLLRPLQYGSTYLIVPATA-------IAVGVCTVA 539

Query: 192 LFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFWALLLAVAMTSTGVAACGPISFIGL 251
             L   L   R L++L LG   A  LGV     R   L +A  +T+      GP+SF+GL
Sbjct: 540 AVLVAYLG-ARWLEILPLGANVADALGVGAQRARLLLLAVAAILTAGATVVIGPMSFVGL 598

Query: 252 VVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLARIIHPPLELPVGVLTAIIGAPWFV 311
           + PH+ R +   R R  + V+AL G LL+V++D L R +  P ++P GV+  ++G P+ +
Sbjct: 599 MAPHLARLLGFPRARSQMLVAALIGGLLMVLSDWLGRNMIFPQQMPAGVIATLLGGPYLM 658

Query: 312 WLLVR 316
           WLL R
Sbjct: 659 WLLRR 663



 Score =  125 bits (315), Expect = 2e-33
 Identities = 91/272 (33%), Positives = 143/272 (52%), Gaps = 8/272 (2%)

Query: 52  LPRLLLALFVGAALAVAGVLIQGIVRNPLASPDILGVNHAASLASVGALLLMPSLPVMVL 111
           LPR+ +AL  GAAL++AGV+ Q ++RNPLA P  LGV+  A LA   A ++ P+L   + 
Sbjct: 65  LPRVAIALIAGAALSLAGVVFQQVLRNPLAEPLTLGVSAGAYLALTIAAVVAPALVADMR 124

Query: 112 PLLAFAGGMAGLILLKMLAKTHQP----MKLALTGVALSACWASLTDYLMLSRPQDVNNA 167
             +A  G  A L +L  +A T +     + + L G+ ++    +L+  L +   + + + 
Sbjct: 125 FTVALTG--AALAMLATMAMTWRKGFAAVSIVLAGMIVNLYCGALSVLLTIVFERSLTSV 182

Query: 168 LLWLTGSLWGRDWSFVKIAIPLMILFLPLSLSFCRDLDLLALGDARATTLGVSVPHTRFW 227
            +W  GSL    W+ V   +P ++     +    R L L +L D  A+ LG+S+  TR  
Sbjct: 183 FIWGGGSLVQNGWAGVVWLLPRVLACGAAAALLVRPLTLFSLDDGSASQLGMSLAWTRPV 242

Query: 228 ALLLAVAMTSTGVAACGPISFIGLVVPHMMRSITGGRHRRLLPVSALTGALLLVVADLLA 287
           AL +AV +++   +A G I FIGL  P + R +   R R  L  + L GALLL +AD   
Sbjct: 243 ALAIAVILSAFVASAVGVIGFIGLGGPVLARLMGARRLRDQLLWAPLVGALLLAIADQAV 302

Query: 288 RIIHPPLE--LPVGVLTAIIGAPWFVWLLVRM 317
           + +   L   LP G   A+ G P  +W+L R+
Sbjct: 303 QSLPGVLGELLPTGAAVALCGGPLLLWMLRRL 334


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: 580
Number of extensions: 27
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: 663
Length adjustment: 33
Effective length of query: 285
Effective length of database: 630
Effective search space:   179550
Effective search space used:   179550
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