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 The sucrose porter, PtsS (regulated by SugR which also regulates other enzymes II) (characterized)
to candidate 18265 b4240 fused trehalose(maltose)-specific PTS enzyme: IIB component/IIC component (NCBI)

Query= TCDB::Q8NMD6
         (661 letters)



>FitnessBrowser__Keio:18265
          Length = 473

 Score =  252 bits (644), Expect = 2e-71
 Identities = 137/448 (30%), Positives = 240/448 (53%), Gaps = 10/448 (2%)

Query: 9   RILRDIGGEDNIVAAAHCATRLRLVLKDTKDVDRQSLDDDPDLKGTFETGGMFQIIVGPG 68
           R++  +GG  NI   +HC TRLR VL    +   + ++  P +KG F   G FQ+++G  
Sbjct: 12  RLIELVGGRGNIATVSHCITRLRFVLNQPANARPKEIEQLPMVKGCFTNAGQFQVVIGTN 71

Query: 69  DVDHVFKELDDATSKDIAVSTEQLKDVVANNANWFSRAVKVLADIFVPLIPILVGGGLLM 128
             D+    +  A++    V  EQ+K    +N  W  + +   A IF PL+P L+ GGL++
Sbjct: 72  VGDYYQALI--ASTGQAQVDKEQVKKAARHNMKWHEQLISHFAVIFFPLLPALISGGLIL 129

Query: 129 AINNVLVAQDLFGPQSLVEMFPQISGVAEMINLMASAPFAFLPVLVGFTATKRFGGNEFL 188
              NV+    +   Q+L +M+P +  + + + L+  A F +LPV + ++A K+ GG   L
Sbjct: 130 GFRNVIGDLPMSNGQTLAQMYPSLQTIYDFLWLIGEAIFFYLPVGICWSAVKKMGGTPIL 189

Query: 189 GAGIGMAMVFPSLVNGYDVAATMAAGEMP-MWSLFGLDVAQAGYQGTVLPVLVVSWILAT 247
           G  +G+ +V P L+N Y     +   ++P +W      +A+ GYQ  V+P L+    L  
Sbjct: 190 GIVLGVTLVSPQLMNAY-----LLGQQLPEVWDFGMFSIAKVGYQAQVIPALLAGLALGV 244

Query: 248 IEKFLHKRLKGTADFLITPVLTLLLTGFLTFIAIGPAMRWVGDVLAHGLQGLYDFG-GPV 306
           IE  L + +      ++ PV +L+L  FL    IGP  R +GD +A  ++ L      P+
Sbjct: 245 IETRLKRIVPDYLYLVVVPVCSLILAVFLAHALIGPFGRMIGDGVAFAVRHLMTGSFAPI 304

Query: 307 GGLLFGLVYSPIVITGLHQSFPPIELELF-NQGGSFIFATASMANIAQGAACLAVFFLAK 365
           G  LFG +Y+P+VITG+HQ+   I+L++  + GG+ ++   +++NIAQG+A + +   ++
Sbjct: 305 GAALFGFLYAPLVITGVHQTTLAIDLQMIQSMGGTPVWPLIALSNIAQGSAVIGIIISSR 364

Query: 366 SEKLKGLAGASGVSAVLGITEPAIFGVNLRLRWPFFIGIGTAAIGGALIALFNIKAVALG 425
               + ++  + +SA LG+TEPA++G+NL+ R+P    +  + + G L  L  + A  +G
Sbjct: 365 KHNEREISVPAAISAWLGVTEPAMYGINLKYRFPMLCAMIGSGLAGLLCGLNGVMANGIG 424

Query: 426 AAGFLGVVSIDAPDMVMFLVCAVVTFFI 453
             G  G++SI      +F +   +   I
Sbjct: 425 VGGLPGILSIQPSYWQVFALAMAIAIII 452


Lambda     K      H
   0.322    0.139    0.408 

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: 669
Number of extensions: 33
Number of successful extensions: 5
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: 661
Length of database: 473
Length adjustment: 36
Effective length of query: 625
Effective length of database: 437
Effective search space:   273125
Effective search space used:   273125
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 (21.9 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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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