GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG in Escherichia coli BW25113

Align PTS system glucose-specific EIICB component; EIICB-Glc; EII-Glc; EC 2.7.1.199 (characterized)
to candidate 15742 b1621 fused maltose and glucose-specific PTS enzymes: IIB component -! IIC component (NCBI)

Query= SwissProt::P37439
         (477 letters)



>FitnessBrowser__Keio:15742
          Length = 530

 Score =  277 bits (708), Expect = 7e-79
 Identities = 182/510 (35%), Positives = 269/510 (52%), Gaps = 53/510 (10%)

Query: 10  QKVGKSLMLPVSVLPIAGILLGVGSANFSW-----LPAVVSHV-------MAEAGGSVFA 57
           Q++GK+ MLPV++L   GI+LG+GS+  S      +P + + V       M++ G   F+
Sbjct: 16  QQLGKTFMLPVALLSFCGIMLGIGSSLSSHDVITLIPVLGNPVLQAIFTWMSKIGSFAFS 75

Query: 58  NMPLIFAIGVALGFTN-NDGVSALAAVVAYGIMVKTM-----------AVVAPLVLHLPA 105
            +P++F I + LG    N GV+A A  + Y +M   +              A ++     
Sbjct: 76  FLPVMFCIAIPLGLARENKGVAAFAGFIGYAVMNLAVNFWLTNKGILPTTDAAVLKANNI 135

Query: 106 EEIAAKHLADTGVLGGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTG 165
           + I      DTG+LG +I+G I   +  RF+ I+LP+ L FF G RFVPIIS L     G
Sbjct: 136 QSILGIQSIDTGILGAVIAGIIVWMLHERFHNIRLPDALAFFGGTRFVPIISSLVMGLVG 195

Query: 166 VVLSFVWPPIGTAIQAFSQWAAYQNPVVAFG--IYGFIERCLVPFGLHHIWNVPFQM-QI 222
           +V+  VWP     I          N    FG  ++G  ER L+PFGLHHI     +    
Sbjct: 196 LVIPLVWPIFAMGISGLGHMI---NSAGDFGPMLFGTGERLLLPFGLHHILVALIRFTDA 252

Query: 223 GEYTNAAGQVFHGDIPRYMAG-----------DPTAGMLSGGFLFKMYGLPAAAIAIWHS 271
           G      GQ   G +  + A              T  +  G     + GLP AA+A++H 
Sbjct: 253 GGTQEVCGQTVSGALTIFQAQLSCPTTHGFSESATRFLSQGKMPAFLGGLPGAALAMYHC 312

Query: 272 AKPENRAKVGGIMISAALTSFLTGITEPIEFSFMFVAPILYIIHAILAGLAFPICILLGM 331
           A+PENR K+ G++IS  +   + G TEP+EF F+FVAP+LY+IHA+L GL F +  +LG+
Sbjct: 313 ARPENRHKIKGLLISGLIACVVGGTTEPLEFLFLFVAPVLYVIHALLTGLGFTVMSVLGV 372

Query: 332 RDGTSFSHGLIDFIV---LSGNSSKLWLFPIVGAGYAIVYYTVFRVLIKALDLKTPGRE- 387
             G +    +IDF+V   L G S+K ++ P+V A + +VYY +FR  I   +LKTPGR+ 
Sbjct: 373 TIGNT-DGNIIDFVVFGILHGLSTKWYMVPVVAAIWFVVYYVIFRFAITRFNLKTPGRDS 431

Query: 388 ---DTTDDAKAGATSEM---APALVAAFGGKENITNLDACITRLRVSVADVAKVDQAGLK 441
               + + A AGA  +     PA++ A GG +NI +LD CITRLR+SV D++ V+   LK
Sbjct: 432 EVASSIEKAVAGAPGKSGYNVPAILEALGGADNIVSLDNCITRLRLSVKDMSLVNVQALK 491

Query: 442 KLGAAGVVVAGS-GVQAIFGTKSDNLKTEM 470
              A GVV      +Q + G +  ++K EM
Sbjct: 492 DNRAIGVVQLNQHNLQVVIGPQVQSVKDEM 521


Lambda     K      H
   0.325    0.140    0.421 

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: 803
Number of extensions: 52
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: 477
Length of database: 530
Length adjustment: 34
Effective length of query: 443
Effective length of database: 496
Effective search space:   219728
Effective search space used:   219728
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 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