Aligments for a candidate for ptsG-crr in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Aligments for a candidate for ptsG-crr in Escherichia coli BW25113

Align PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized)
to candidate 15742 b1621 fused maltose and glucose-specific PTS enzymes: IIB component -! IIC component (NCBI)

Query= CharProtDB::CH_001857
         (699 letters)



>FitnessBrowser__Keio:15742
          Length = 530

 Score =  339 bits (870), Expect = 2e-97
 Identities = 197/522 (37%), Positives = 304/522 (58%), Gaps = 19/522 (3%)

Query: 5   LFGVLQKIGRALMLPVAILPAAGILLAIGNAMQNKDMIQVLHFLSNDNVQLVAGVMESAG 64
           L+   Q++G+  MLPVA+L   GI+L IG+++ + D+I ++  L N  +Q +   M   G
Sbjct: 11  LWEFFQQLGKTFMLPVALLSFCGIMLGIGSSLSSHDVITLIPVLGNPVLQAIFTWMSKIG 70

Query: 65  QIVFDNLPLLFAVGVAIGLANGD-GVAGIAAIIGYLVMNVSMSAVLLANGTIPSDSVERA 123
              F  LP++F + + +GLA  + GVA  A  IGY VMN++++  L   G +P+     A
Sbjct: 71  SFAFSFLPVMFCIAIPLGLARENKGVAAFAGFIGYAVMNLAVNFWLTNKGILPTTD---A 127

Query: 124 KFFTENHPAYVNMLGIPTLATGVFGGIIVGVLAALLFNRFYTIELPQYLGFFAGKRFVPI 183
                N+    ++LGI ++ TG+ G +I G++  +L  RF+ I LP  L FF G RFVPI
Sbjct: 128 AVLKANN--IQSILGIQSIDTGILGAVIAGIIVWMLHERFHNIRLPDALAFFGGTRFVPI 185

Query: 184 VTSISALILGLIMLVIWPPIQHGLNAFSTGLVEANPTLAAFIFGVIERSLIPFGLHHIFY 243
           ++S+   ++GL++ ++WP    G++     ++ +       +FG  ER L+PFGLHHI  
Sbjct: 186 ISSLVMGLVGLVIPLVWPIFAMGISGLGH-MINSAGDFGPMLFGTGERLLLPFGLHHILV 244

Query: 244 SPFWY-EFFSYKSAAGEIIRGDQRIFMAQIK----DGVQLTAGTFMT-GKYPFMMFGLPA 297
           +   + +    +   G+ + G   IF AQ+      G   +A  F++ GK P  + GLP 
Sbjct: 245 ALIRFTDAGGTQEVCGQTVSGALTIFQAQLSCPTTHGFSESATRFLSQGKMPAFLGGLPG 304

Query: 298 AALAIYHEAKPQNKKLVAGIMGSAALTSFLTGITEPLEFSFLFVAPVLFAIHCLFAGLSF 357
           AALA+YH A+P+N+  + G++ S  +   + G TEPLEF FLFVAPVL+ IH L  GL F
Sbjct: 305 AALAMYHCARPENRHKIKGLLISGLIACVVGGTTEPLEFLFLFVAPVLYVIHALLTGLGF 364

Query: 358 MVMQLLNVKIGMTFSGGLIDYFLFGILPNRTAWWLVIPVGLGL-AVIYYFGFRFAIRKFN 416
            VM +L V IG T  G +ID+ +FGIL   +  W ++PV   +  V+YY  FRFAI +FN
Sbjct: 365 TVMSVLGVTIGNT-DGNIIDFVVFGILHGLSTKWYMVPVVAAIWFVVYYVIFRFAITRFN 423

Query: 417 LKTPGRED---AAEETAAPGKTGEAGDLPYEILQAMGDQENIKHLDACITRLRVTVNDQK 473
           LKTPGR+    ++ E A  G  G++G     IL+A+G  +NI  LD CITRLR++V D  
Sbjct: 424 LKTPGRDSEVASSIEKAVAGAPGKSGYNVPAILEALGGADNIVSLDNCITRLRLSVKDMS 483

Query: 474 KVDKDRLKQLGASGVLEVG-NNIQAIFGPRSDGLKTQMQDII 514
            V+   LK   A GV+++  +N+Q + GP+   +K +M  ++
Sbjct: 484 LVNVQALKDNRAIGVVQLNQHNLQVVIGPQVQSVKDEMAGLM 525


Lambda     K      H
   0.323    0.141    0.412 

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: 982
Number of extensions: 63
Number of successful extensions: 10
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: 699
Length of database: 530
Length adjustment: 37
Effective length of query: 662
Effective length of database: 493
Effective search space:   326366
Effective search space used:   326366
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 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