Alignments for a candidate for PS417_11890 in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Escherichia coli BW25113

Align Inositol transport system ATP-binding protein (characterized)
to candidate 16258 b2149 fused methyl-galactoside transporter subunits of ABC superfamily: ATP-binding components (NCBI)

Query= reanno::WCS417:GFF2332
         (517 letters)



>FitnessBrowser__Keio:16258
          Length = 506

 Score =  467 bits (1202), Expect = e-136
 Identities = 243/493 (49%), Positives = 345/493 (69%), Gaps = 4/493 (0%)

Query: 22  YLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIR 81
           YLLE+  I+K FPGV AL +V L+VRP ++ ALMGENGAGKSTL+K + GIYQ D+G I 
Sbjct: 12  YLLEMSGINKSFPGVKALDNVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTIL 71

Query: 82  LRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCT 141
            +GK I F +   A + GI+M+HQELNL+   S+ +N+W+GR     +  V+  +M+R T
Sbjct: 72  FQGKEIDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKGM-FVDQDKMYRET 130

Query: 142 AELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201
             +   L I++DP  +VG LS+++ QM+EIAKA SY++ I+IMDEPTS++TEKEV HLF+
Sbjct: 131 KAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFT 190

Query: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261
           II  LK +G GIVYI+HKM E+F + DEV V RDG +I  +    +  D +I+MMVGR L
Sbjct: 191 IIRKLKERGCGIVYISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVGRSL 250

Query: 262 SQLFPLRETPIGDLLLTVRDLT--LDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIF 319
           +Q FP +E   G+++L VR+LT       +DVSFDLH GEILGIAGL+G+ RT++ ET+F
Sbjct: 251 NQRFPDKENKPGEVILEVRNLTSLRQPSIRDVSFDLHKGEILGIAGLVGAKRTDIVETLF 310

Query: 320 GITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHY 379
           GI   S+G ITL GK +   + + AI  GFAL+TE+R+ +G++  L +  N  ++ + +Y
Sbjct: 311 GIREKSAGTITLHGKQINNHNANEAINHGFALVTEERRSTGIYAYLDIGFNSLISNIRNY 370

Query: 380 TGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLIL 438
               G +    +++  + +   +RVKTP     I +LSGGNQQK ++ RWL+T P +L+L
Sbjct: 371 KNKVGLLDNSRMKSDTQWVIDSMRVKTPGHRTQIGSLSGGNQQKVIIGRWLLTQPEILML 430

Query: 439 DEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDR 498
           DEPTRGIDVGAK EIY+LIA LA +G  +I+ISSE+PE+LG++DR++VM  G + G +D 
Sbjct: 431 DEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGITDRILVMSNGLVSGIVDT 490

Query: 499 SEATQEKVMQLAS 511
              TQ ++++LAS
Sbjct: 491 KTTTQNEILRLAS 503



 Score = 74.3 bits (181), Expect = 1e-17
 Identities = 51/223 (22%), Positives = 104/223 (46%), Gaps = 6/223 (2%)

Query: 290 DVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGF 349
           +V+  +    I  + G  G+G++ + + +FGI    SG I   GK +       A+E G 
Sbjct: 31  NVNLKVRPHSIHALMGENGAGKSTLLKCLFGIYQKDSGTILFQGKEIDFHSAKEALENGI 90

Query: 350 ALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLE 409
           +++ ++  L       SV++NM +   P  T   F+ Q  +    + +  +L +      
Sbjct: 91  SMVHQELNL---VLQRSVMDNMWLGRYP--TKGMFVDQDKMYRETKAIFDELDIDIDPRA 145

Query: 410 QCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIM 469
           + + TLS    Q   +A+    N +++I+DEPT  +       ++ +I  L   G  ++ 
Sbjct: 146 R-VGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTEKEVNHLFTIIRKLKERGCGIVY 204

Query: 470 ISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512
           IS ++ E+  + D V V+ +G+ + T   +  T +K++ +  G
Sbjct: 205 ISHKMEEIFQLCDEVTVLRDGQWIATEPLAGLTMDKIIAMMVG 247


Lambda     K      H
   0.320    0.136    0.381 

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: 658
Number of extensions: 31
Number of successful extensions: 8
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: 517
Length of database: 506
Length adjustment: 35
Effective length of query: 482
Effective length of database: 471
Effective search space:   227022
Effective search space used:   227022
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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
the source code
instructions for running GapMind on your computer

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