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

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources