GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagEcba in Shewanella amazonensis SB2B

Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate 6936959 Sama_1133 PTS system, glucose-specific IIBC component (RefSeq)

Query= BRENDA::P09323
         (648 letters)



>FitnessBrowser__SB2B:6936959
          Length = 485

 Score =  287 bits (734), Expect = 9e-82
 Identities = 168/479 (35%), Positives = 271/479 (56%), Gaps = 41/479 (8%)

Query: 6   FFQRLGRALQLPIAVLPVAALLLRFGQ------PDLLNVAFIAQAGGAIFDNLALIFAIG 59
           F QRL + L +PIA+LP A +++          PD+ NV  ++  G  IFD + ++FAI 
Sbjct: 22  FAQRLSQTLLIPIAILPAAGVMIGIATNPLPFIPDVANVLMLS-VGKLIFDIMPMLFAIA 80

Query: 60  VASSWSKDSAGAAALAGAVGYFVLTKAMVTI-------------NPEINMGVLAGIITGL 106
           VA  + +D  G AA + A GY VL   +                 P I+ G+  G++ G 
Sbjct: 81  VAIGFCRDQ-GIAAFSAAFGYGVLLSTLAAAAKVYHLPSHIVWGTPTIDTGIAGGMLVGG 139

Query: 107 VGGAAYNRWSDIKLPDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQHAIHAGGEWI 166
           +   A      ++LP   SFF G+R  P+      ++LA +  ++WPP+  +I    +W 
Sbjct: 140 ITCVAVRLSEKLRLPAVFSFFEGRRSAPLIMIPLVMLLAVMLAFIWPPLALSIERLSDWA 199

Query: 167 V-SAGALGSGIFGFINRLLIPTGLHQVLNTIAWFQIGEFTNAAGTVFHGDINRFYAGDGT 225
           V    A+  G +G + RLL+P GLH + N   + ++G++ +  G +  G++ R++AGD +
Sbjct: 200 VYQEPAIAFGFYGMVERLLLPLGLHHIWNAPFYLEVGQYAHD-GEIVRGEMARYFAGDPS 258

Query: 226 AGMFMSGFFPIMMFGLPGAALAMYFAAPKERRPMVGGMLLSVAVTAFLTGVTEPLEFLFM 285
           AG    G+  I M+GLP AALA++  A + +R  V G++LS A  ++LTGVTEP+EF F+
Sbjct: 259 AGNLAGGYL-IKMWGLPAAALAIWRCADRNQRNRVAGVMLSAATASWLTGVTEPIEFAFL 317

Query: 286 FLAPLLYLLHALLTGISLFVATLLGIHAGFSFSAGAIDYALMYNLPAASQNVWMLLVMGV 345
           F+APLLYL HALLTG++  +A LL +H    FS G +D+ L++  P +S   W +  +G 
Sbjct: 318 FVAPLLYLCHALLTGLAYSIAILLDMHHSVVFSHGLVDFVLLF--PQSSNTHW-IWFLGP 374

Query: 346 IFFAIYFVVFSLVIRMFNLKTPGREDKEDEIVTEEANSNTEEGLTQLATNYIAAVGGTDN 405
           + F IY+++F   I  FNLKTPGR          EA++  +  L  +    ++A+GG  N
Sbjct: 375 LTFVIYYILFRASILAFNLKTPGR---------FEADTGQKRNLIAI----VSALGGGGN 421

Query: 406 LKAIDACITRLRLTVADSARVNDTMCKRLGASGVVKLNKQTIQVIVGAKAESIGDAMKK 464
           +  + AC+TRLR++VAD ++V+      LGA GV+ +    +Q++ G KAE++   +++
Sbjct: 422 IADLSACLTRLRISVADPSQVDRQRLMSLGAKGVIVVG-SGVQLVFGTKAETLRKLLQR 479


Lambda     K      H
   0.324    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: 661
Number of extensions: 27
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: 648
Length of database: 485
Length adjustment: 36
Effective length of query: 612
Effective length of database: 449
Effective search space:   274788
Effective search space used:   274788
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: 41 (22.0 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