Alignments for a candidate for xylG in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylG in Escherichia coli BW25113

Align Xylose import ATP-binding protein XylG; EC 7.5.2.10 (characterized)
to candidate 17809 b3749 fused D-ribose transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= SwissProt::P37388
         (513 letters)



>FitnessBrowser__Keio:17809
          Length = 501

 Score =  436 bits (1120), Expect = e-126
 Identities = 232/512 (45%), Positives = 335/512 (65%), Gaps = 12/512 (2%)

Query: 1   MPYLLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYE 60
           M  LL++K I K F  VKA+    L +  G +++L GENG+GKST+MKVL GIY   +  
Sbjct: 1   MEALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDA-- 58

Query: 61  GEIIFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEITHN-GIMDYDLM 119
           G +++ G+E   +  + ++  GI IIHQEL L+ +LT+ ENIFLG E  +  G +D+  M
Sbjct: 59  GTLLWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTM 118

Query: 120 TLRCQKLLAQVSLSISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETS 179
                KLLA+++L    D  VGDL +G QQ+VEIAK L+ + +++I+DEPT +LT+ ET 
Sbjct: 119 YAEADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETE 178

Query: 180 ILLDIIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMV 239
            L  +IR+L+  G   +YISH++ E+  I D + V RDGQ I  R+ A ++ED +I MMV
Sbjct: 179 SLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMV 238

Query: 240 GRELTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAG 299
           GR+L   YP+     GD  L++++L            VNDVSF+L++GEILG++GL+GAG
Sbjct: 239 GRKLEDQYPHLDKAPGDIRLKVDNLCG--------PGVNDVSFTLRKGEILGVSGLMGAG 290

Query: 300 RTETIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGK 359
           RTE ++ L+G  P +  G + +DG +V  R+ Q  +A GI  + EDRKRDG+V  M+V +
Sbjct: 291 RTELMKVLYGALP-RTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKE 349

Query: 360 NITLAALNKFTGGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILARC 419
           N++L AL  F+     L  A EQ+ + + I+   VKT S + AIG LSGGNQQK  +AR 
Sbjct: 350 NMSLTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARG 409

Query: 420 LLLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMH 479
           L+  P++LILDEPTRG+D+GAK EIY+LINQ    G+++I++SSE+PEVLG+SDR++VMH
Sbjct: 410 LMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMH 469

Query: 480 EGKLKANLINHNLTQEQVMEAALRSEHHVEKQ 511
           EG L         TQE +M AA+   + V ++
Sbjct: 470 EGHLSGEFTREQATQEVLMAAAVGKLNRVNQE 501


Lambda     K      H
   0.319    0.137    0.391 

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: 650
Number of extensions: 32
Number of successful extensions: 9
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: 513
Length of database: 501
Length adjustment: 34
Effective length of query: 479
Effective length of database: 467
Effective search space:   223693
Effective search space used:   223693
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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:

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