GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manP in Escherichia coli BW25113

Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate 17939 b3899 PTS system, fructose-like enzyme IIBC component (VIMSS)

Query= BRENDA::O31645
         (650 letters)



>FitnessBrowser__Keio:17939
          Length = 483

 Score =  286 bits (731), Expect = 2e-81
 Identities = 166/471 (35%), Positives = 264/471 (56%), Gaps = 24/471 (5%)

Query: 1   MKLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAII 60
           ++++AIT+CP GIAHTYM AE L++ A  LG +IKVETQG  GVEN+L+ EEI  AD +I
Sbjct: 5   LRIVAITNCPAGIAHTYMVAEALEQKARSLGHTIKVETQGSSGVENRLSSEEIAAADYVI 64

Query: 61  IAADRSVNKD---RFIGKKLLSVGVQDGIRKPEELIQKALNGDIPVYRSATKSESG---N 114
           +A  R ++ D   RF GKK+  + +   ++  +++       ++P       ++SG    
Sbjct: 65  LATGRGLSGDDRARFAGKKVYEIAISQALKNIDQIFS-----ELPTNSQLFAADSGVKLG 119

Query: 115 HQEKKQNPIYRHLMNGVSFMVPFIVVGGLLIAVALTLGGEKTPKGLVIPD-----DSFWK 169
            QE +   +  HLM GVS  +PF++ GG+L+A+A  L       GL   D      SF  
Sbjct: 120 KQEVQSGSVMSHLMAGVSAALPFVIGGGILVALANML----VQFGLPYTDMSKGAPSFTW 175

Query: 170 TIEQIGSASFSFMIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGII 229
            +E IG   F+FMIPI+  YIA SIADKP   P  +  Y+A   +   + SGAGFLG ++
Sbjct: 176 VVESIGYLGFTFMIPIMGAYIASSIADKPAFAPAFLVCYLANDKALLGTQSGAGFLGAVV 235

Query: 230 AGFLAGYAALWIKKLKVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVW 289
            G   GY   W +K+++ KA+QP++  ++IP    L+ G+   ++IG  ++ +   L  +
Sbjct: 236 LGLAIGYFVFWFRKVRLGKALQPLLGSMLIPFVTLLVFGVLTYYVIGPVMSDLMGGLLHF 295

Query: 290 LAGMKGSSSILLALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAICIPPI 349
           L  +  S     A ++GAM++FDMGGP+NK A+ F  +++ +  Y+    + V   +PP+
Sbjct: 296 LNTIPPSMKFAAAFLVGAMLAFDMGGPINKTAWFFCFSLLEKHIYDWYAIVGVVALMPPV 355

Query: 350 GLGIATFLGKRKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVI-PSIMAGSMTGS 408
             G+ATF+  + F   ++E   +A  +G    TE AIP+A   PL +I  + +AG +TG 
Sbjct: 356 AAGLATFIAPKLFTRQEKEAASSAIVVGATVATEPAIPYALAAPLPMITANTLAGGITGV 415

Query: 409 VIAMIGNVGDRVAHG-GPIVAVLGAVDHVLMFFIAVIAGSLVTALFVNVLK 458
           ++   G    R+A G G    ++G +  V  F++ +  G  +   F+ VLK
Sbjct: 416 LVIAFGI--KRLAPGLGIFDPLIGLMSPVGSFYLVLAIGLALNISFIIVLK 464


Lambda     K      H
   0.319    0.137    0.386 

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: 719
Number of extensions: 35
Number of successful extensions: 4
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: 650
Length of database: 483
Length adjustment: 36
Effective length of query: 614
Effective length of database: 447
Effective search space:   274458
Effective search space used:   274458
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 (21.7 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