GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Keio:17809 b3749 fused D-ribose transporter
           subunits of ABC superfamily: ATP-binding components
           (NCBI)
          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.

Links

Downloads

Related tools

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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