GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagB in Frischella perrara PEB0191

Align glucosamine-6-phosphate deaminase (EC 3.5.99.6) (characterized)
to candidate WP_039103138.1 FPB0191_RS00155 glucosamine-6-phosphate deaminase

Query= BRENDA::P0A759
         (266 letters)



>NCBI__GCF_000807275.1:WP_039103138.1
          Length = 268

 Score =  393 bits (1009), Expect = e-114
 Identities = 179/264 (67%), Positives = 228/264 (86%)

Query: 1   MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQ 60
           MRLIPL  ++++G WAA +IV +IN F PTA+RPFVLGLPTG +P+  Y+ L++ ++AG 
Sbjct: 1   MRLIPLKHSQEIGAWAADYIVKKINDFNPTAERPFVLGLPTGSSPLVMYQQLIKRYQAGL 60

Query: 61  VSFKHVVTFNMDEYVGLPKEHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQ 120
           VSFKHVVTFNMDEYVG+P++HP+SY++FM++NFF+H+DI   NIN+L+GNA DI  EC +
Sbjct: 61  VSFKHVVTFNMDEYVGIPEDHPQSYHTFMYQNFFNHIDINKNNINILDGNAQDIVKECEE 120

Query: 121 YEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFDNDVNQ 180
           YE KI+SYGKI LF+GGVG DGHIAFNEP SSL SRTRIKTLT DTR+ANSRFFDND+ Q
Sbjct: 121 YEAKIKSYGKIDLFIGGVGQDGHIAFNEPGSSLCSRTRIKTLTEDTRIANSRFFDNDITQ 180

Query: 181 VPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIMVCD 240
           VP+YALT+GVGTL+DA+EVM+L+ G  KA+ALQ AVEG VNH+WT+S LQ+H K+++VCD
Sbjct: 181 VPEYALTIGVGTLMDAKEVMLLISGHNKAIALQQAVEGAVNHLWTVSALQMHAKSLIVCD 240

Query: 241 EPSTMELKVKTLRYFNELEAENIK 264
           EPST ELKVKTL+YF +LEA+N++
Sbjct: 241 EPSTDELKVKTLKYFKQLEAKNLE 264


Lambda     K      H
   0.320    0.135    0.405 

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: 267
Number of extensions: 8
Number of successful extensions: 1
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: 266
Length of database: 268
Length adjustment: 25
Effective length of query: 241
Effective length of database: 243
Effective search space:    58563
Effective search space used:    58563
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 (21.8 bits)
S2: 47 (22.7 bits)

Align candidate WP_039103138.1 FPB0191_RS00155 (glucosamine-6-phosphate deaminase)
to HMM TIGR00502 (nagB: glucosamine-6-phosphate deaminase (EC 3.5.99.6))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR00502.hmm
# target sequence database:        /tmp/gapView.296868.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00502  [M=259]
Accession:   TIGR00502
Description: nagB: glucosamine-6-phosphate deaminase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                             Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.1e-137  440.7   0.2   9.2e-137  440.5   0.2    1.0  1  NCBI__GCF_000807275.1:WP_039103138.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000807275.1:WP_039103138.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  440.5   0.2  9.2e-137  9.2e-137       1     259 []       1     259 [.       1     259 [. 1.00

  Alignments for each domain:
  == domain 1  score: 440.5 bits;  conditional E-value: 9.2e-137
                             TIGR00502   1 mklliletyeelsklaariiaekinefkpdaerpfvlGlatGgtPvglykqlielykagkvsfkkvvtfnlde 73 
                                           m+l++l++ +e++ +aa +i++kin+f+p+aerpfvlGl+tG++P+ +y+qli+ y+ag vsfk+vvtfn+de
  NCBI__GCF_000807275.1:WP_039103138.1   1 MRLIPLKHSQEIGAWAADYIVKKINDFNPTAERPFVLGLPTGSSPLVMYQQLIKRYQAGLVSFKHVVTFNMDE 73 
                                           9************************************************************************ PP

                             TIGR00502  74 yvglseehPesyhsfmyenffqhidikpeninilnGnaddleaecrryeekikslGkidlfllGiGadGhiaf 146
                                           yvg++e+hP+syh+fmy+nff+hidi+++ninil+Gna+d+ +ec++ye kiks+Gkidlf++G+G+dGhiaf
  NCBI__GCF_000807275.1:WP_039103138.1  74 YVGIPEDHPQSYHTFMYQNFFNHIDINKNNINILDGNAQDIVKECEEYEAKIKSYGKIDLFIGGVGQDGHIAF 146
                                           ************************************************************************* PP

                             TIGR00502 147 nePgsslesrtrvktltedtiiansrffegdvnkvPkkaltvGiktildskevlllvsGkekaeavkklvegs 219
                                           nePgssl srtr+ktltedt+iansrff++d+++vP +alt+G++t++d+kev+ll+sG++ka a++++veg+
  NCBI__GCF_000807275.1:WP_039103138.1 147 NEPGSSLCSRTRIKTLTEDTRIANSRFFDNDITQVPEYALTIGVGTLMDAKEVMLLISGHNKAIALQQAVEGA 219
                                           ************************************************************************* PP

                             TIGR00502 220 vnedvtisalqlhkkvivvadeeaaqelkvktlkyfnele 259
                                           vn+++t+salq+h k ++v+de ++ elkvktlkyf++le
  NCBI__GCF_000807275.1:WP_039103138.1 220 VNHLWTVSALQMHAKSLIVCDEPSTDELKVKTLKYFKQLE 259
                                           *************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (259 nodes)
Target sequences:                          1  (268 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 16.69
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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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