Alignments for a candidate for ptsS in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for ptsS in Escherichia coli BW25113

Align protein-Npi-phosphohistidine-sucrose phosphotransferase (EC 2.7.1.211) (characterized)
to candidate 17782 b3722 fused beta-glucoside-specific PTS enzymes: IIA component/IIB component/IIC component (NCBI)

Query= BRENDA::P12655
         (664 letters)



>FitnessBrowser__Keio:17782
          Length = 625

 Score =  313 bits (802), Expect = 2e-89
 Identities = 219/666 (32%), Positives = 332/666 (49%), Gaps = 51/666 (7%)

Query: 4   SKVASEVITAVG-KDNLVAAAHCATRLRLVLKDDSKVDQKALDKNADVKGTFKTDGQYQV 62
           +++A +++  VG  DN+V+  HCATRLR  LKD+SK   + L K   +    ++ GQ+QV
Sbjct: 2   TELARKIVAGVGGADNIVSLMHCATRLRFKLKDESKAQAEVLKKTPGIIMVVESGGQFQV 61

Query: 63  IIGPGDVNFVYDEIIKQTGLTEVSTDDLKKIAASGKKFNPIMALIKLLSDIFVPIIPALV 122
           +IG   V  V+  +    GL E +    ++   +  K N +   + ++S IF P+I  + 
Sbjct: 62  VIG-NHVADVFLAVNSVAGLDEKA----QQAPENDDKGNLLNRFVYVISGIFTPLIGLMA 116

Query: 123 AGGLLMALNNFLTSEGLFGTKSLVQQFPIIKGSSDMIQLMSAAPFWFLPILVGISAAKRF 182
           A G+L         +G+       Q      G+  ++   S A FWF PI++G +A KRF
Sbjct: 117 ATGIL---------KGMLALALTFQWTTEQSGTYLILFSASDALFWFFPIILGYTAGKRF 167

Query: 183 GANQFLGASIGMIMVAPGAANIIGLAANAPISKAATIGAYTGFWNIFGLHVTQASYTYQV 242
           G N F    IG  +V P     + L A     KA  +G      +  G+ VT  +Y+  V
Sbjct: 168 GGNPFTAMVIGGALVHP-----LILTAFENGQKADALGL-----DFLGIPVTLLNYSSSV 217

Query: 243 IPVLVAVWLLSILEKFFHKRLPSAVDFTFTPLLSVIITGFLTFIVIGPVMKEVSDWLTNG 302
           IP++ + WL SILE+  +  LPSA+   FTPLL +++   +TF+++GP+   +S+ +  G
Sbjct: 218 IPIIFSAWLCSILERRLNAWLPSAIKNFFTPLLCLMVITPVTFLLVGPLSTWISELIAAG 277

Query: 303 IVWLYDTTGFLGMGVFGALYSPVVMTGLHQSFPAIETQLISAFQNGTGHG-DFIFVTASM 361
            +WLY         V G  +   VM GLH     +         N T  G D +      
Sbjct: 278 YLWLYQAVPAFAGAVMGGFWQIFVMFGLHWGLVPL------CINNFTVLGYDTMIPLLMP 331

Query: 362 ANVAQGAATFAIYFLTKDKKMKGLSSSSGVSALLGITEPALFGVNLKYRFPFFCALIGSA 421
           A +AQ  A   ++   +D + K ++ S+ +++L GITEPA++GVNL  ++PF  A I  A
Sbjct: 332 AIMAQVGAALGVFLCERDAQKKVVAGSAALTSLFGITEPAVYGVNLPRKYPFVIACISGA 391

Query: 422 SAAAIAGLLQVVAVSLGSAGFLGFL-SIKASSIPFYVVCELISFAIAFAVTYGYGKTKAV 480
             A I G  Q    S G      F+ +I ++ I F V   +I   IA    +  G     
Sbjct: 392 LGATIIGYAQTKVYSFGLPSIFTFMQTIPSTGIDFTVWASVIGGVIAIGCAF-VGTVMLH 450

Query: 481 DVFA----AEAAVEEAIEEVQEIPEEAASAANKAQVTDEVLAAPLAGEAVELTSVNDPVF 536
            + A    A+ A +E   EV   PE+              + +P+ GE V L  V D  F
Sbjct: 451 FITAKRQPAQGAPQEKTPEVITPPEQGG------------ICSPMTGEIVPLIHVADTTF 498

Query: 537 SSEAMGKGIAIKPSGNTVYAPVDGTVQIAFDTGHAYGIKSDNGAEILIHIGIDTVSMEGK 596
           +S  +GKGIAI PS   V +PV G +   F T HA GI+SD+G EILIH+GIDTV ++GK
Sbjct: 499 ASGLLGKGIAILPSVGEVRSPVAGRIASLFATLHAIGIESDDGVEILIHVGIDTVKLDGK 558

Query: 597 GFEQKVQADQKIKKGDVLGTFDSDKIAEAGLDNTTMFIVTNTADYASVETLASSGTVAVG 656
            F   V    K+  GD L +FD   I EAG D TT  +++N+ D+  V     +  ++ G
Sbjct: 559 FFSAHVNVGDKVNTGDRLISFDIPAIREAGFDLTTPVLISNSDDFTDV-LPHGTAQISAG 617

Query: 657 DSLLEV 662
           + LL +
Sbjct: 618 EPLLSI 623


Lambda     K      H
   0.320    0.135    0.384 

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: 1026
Number of extensions: 55
Number of successful extensions: 6
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: 664
Length of database: 625
Length adjustment: 38
Effective length of query: 626
Effective length of database: 587
Effective search space:   367462
Effective search space used:   367462
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: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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
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