GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malEIICBA in Escherichia coli BW25113

Align The maltose/maltotriose porter, MalT (31% identical to 4.A.1.1.9) (characterized)
to candidate 15223 b1101 fused glucose-specific PTS enzymes: IIB component/IIC component (NCBI)

Query= TCDB::Q8DS05
         (729 letters)



>FitnessBrowser__Keio:15223
          Length = 477

 Score =  251 bits (640), Expect = 8e-71
 Identities = 174/550 (31%), Positives = 285/550 (51%), Gaps = 86/550 (15%)

Query: 9   SFEFWQKFGKCLMVVIAVMPAAGLMVSIGNSLALIDPKSTLLVTVANIIAQIGWGVINNL 68
           +F   QK GK LM+ ++V+P AG+++ +G++       S L   V++++A+ G  V  N+
Sbjct: 5   AFANLQKVGKSLMLPVSVLPIAGILLGVGSANF-----SWLPAVVSHVMAEAGGSVFANM 59

Query: 69  HILFAVAIGGSWAKERAGGAFAAALAFILINLITGNFYGISLEMIADKTSYVHNIFGGKM 128
            ++FA+ +   +       A AA +A           YGI ++ +A     V ++   ++
Sbjct: 60  PLIFAIGVALGFTNNDGVSALAAVVA-----------YGIMVKTMAVVAPLVLHLPAEEI 108

Query: 129 ---HVADYFINVLGQPALNMGVFVGIISGFVGATAYNKYYNFRKLPDVLSFFNGKRFVPF 185
              H+AD             GV  GIISG + A  +N++Y   KLP+ L FF GKRFVP 
Sbjct: 109 ASKHLAD------------TGVLGGIISGAIAAYMFNRFYRI-KLPEYLGFFAGKRFVPI 155

Query: 186 VVIVRSTIVALILSVFWPIVQSGINGFGMWIASSQHTAPFLAPFLYGTLERLLLPFGLHH 245
           +  + +    ++LS  WP + S I  F  W A   +  P +A  +YG +ER L+PFGLHH
Sbjct: 156 ISGLAAIFTGVVLSFIWPPIGSAIQTFSQWAA---YQNPVVAFGIYGFIERCLVPFGLHH 212

Query: 246 MLTIPMNYTQLGGTYVVLTGAQAGKHVLGQDPLWLAWVQDLIHLKGAGHMSQYHHLLTSV 305
           +  +P    Q+G      T A AG+   G  P ++A       L G      Y       
Sbjct: 213 IWNVPFQM-QIGE----YTNA-AGQVFHGDIPRYMAGDPTAGKLSGGFLFKMYG------ 260

Query: 306 TPARFKVGQMIGSSGILMGLTLAMYRNVDPDKKEKYKGMFLSAAVAVFLTGVTEPLEYMF 365
                           L    +A++ +  P+ + K  G+ +SAA+  FLTG+TEP+E+ F
Sbjct: 261 ----------------LPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPIEFSF 304

Query: 366 MFAALPLYLVYAVVQGLAFASADLIHLR---VHSFGNIEFLTRTPMAIKAGLAMDIVNFI 422
           MF A  LY+++A++ GLAF    L+ +R     S G I+F+      + +G +  +  F 
Sbjct: 305 MFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFI------VLSGNSSKLWLFP 358

Query: 423 VVSVVFGVAMYFITNFMIKKFNLATSGRNGNYDTGDDASDETASNSNAGTANANSQIVKI 482
           +V + + +  Y I   +IK  +L T GR       +DA+++  +   +  A A      +
Sbjct: 359 IVGIGYAIVYYTIFRVLIKALDLKTPGR-------EDATEDAKATGTSEMAPA------L 405

Query: 483 INLLGGKENISDVDACMTRLRITVTDVAKVGDEAAWKKAGAMGLIVKGNGVQAVYGPKAD 542
           +   GGKENI+++DAC+TRLR++V DV+KV D+A  KK GA G++V G+GVQA++G K+D
Sbjct: 406 VAAFGGKENITNLDACITRLRVSVADVSKV-DQAGLKKLGAAGVVVAGSGVQAIFGTKSD 464

Query: 543 VLKSDIQDLL 552
            LK+++ + +
Sbjct: 465 NLKTEMDEYI 474


Lambda     K      H
   0.322    0.138    0.402 

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: 809
Number of extensions: 42
Number of successful extensions: 7
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: 729
Length of database: 477
Length adjustment: 37
Effective length of query: 692
Effective length of database: 440
Effective search space:   304480
Effective search space used:   304480
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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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:

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:

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:

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:

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