GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__SB2B:6936959 Sama_1133 PTS system,
           glucose-specific IIBC component (RefSeq)
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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