GapMind for catabolism of small carbon sources

 

Alignments for a candidate for BPHYT_RS34245 in Escherichia coli BW25113

Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate 17809 b3749 fused D-ribose transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= uniprot:B2T9V9
         (510 letters)



>FitnessBrowser__Keio:17809
          Length = 501

 Score =  285 bits (729), Expect = 3e-81
 Identities = 166/474 (35%), Positives = 265/474 (55%), Gaps = 10/474 (2%)

Query: 20  VTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTGEVRFSGAAAP 79
           + K F    AL+  ++ V PG   ALVG NGAGKST++ +LTG+   D G + + G    
Sbjct: 10  IDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWLGKETT 69

Query: 80  SIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPL-RGGVIDWQAMRRDARALLDHW 138
               + +    +  ++Q   +I  L++AEN+F+ R+ + R G IDW+ M  +A  LL   
Sbjct: 70  FTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEADKLLAKL 129

Query: 139 KIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFRRISELQR 198
            +  + D   GDLS+  +Q+VEIA+ LS+ ++ II+DEPT  L   E + LFR I EL+ 
Sbjct: 130 NLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIRELKS 189

Query: 199 EGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTGERGGLAVADA 258
           +G   ++ISH ++E++EIC  VTV RD + I    V++L  + LIE M G +    + D 
Sbjct: 190 QGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRK----LEDQ 245

Query: 259 AAR-GALPADTAVALELKELTGADYEGVSFTVKRGEVVGLTGATSSGRTSVAEAIAGLRA 317
                  P D  + L++  L G     VSFT+++GE++G++G   +GRT + + + G   
Sbjct: 246 YPHLDKAPGD--IRLKVDNLCGPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALP 303

Query: 318 AKRGTISVDGAILPPGDVPASLAHGIGCVPKDRHHEGLVLTQSVAENASMTIARVLGKFG 377
              G +++DG  +        LA+GI  + +DR  +GLVL  SV EN S+T  R   + G
Sbjct: 304 RTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAG 363

Query: 378 IAAP-AKKNAFGQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATNPNVLVLIDPT 436
            +   A +       I    +     E  +  LSGGNQQKV +AR L T P VL+L +PT
Sbjct: 364 GSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPT 423

Query: 437 AGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRVAAEF 489
            GVDV +K+ +  ++++ + +G ++++VS E+ + L   DR++VM  G ++ EF
Sbjct: 424 RGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEF 477


Lambda     K      H
   0.318    0.134    0.377 

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: 549
Number of extensions: 31
Number of successful extensions: 8
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: 510
Length of database: 501
Length adjustment: 34
Effective length of query: 476
Effective length of database: 467
Effective search space:   222292
Effective search space used:   222292
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 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