Alignments for a candidate for pgmB in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for pgmB in Dyella japonica UNC79MFTsu3.2

Align Beta-phosphoglucomutase; Beta-PGM; EC 5.4.2.6 (characterized)
to candidate N515DRAFT_1906 N515DRAFT_1906 alpha,alpha-trehalose phosphorylase

Query= SwissProt::P77366
         (219 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1906
          Length = 1036

 Score =  179 bits (453), Expect = 2e-49
 Identities = 95/202 (47%), Positives = 133/202 (65%), Gaps = 4/202 (1%)

Query: 3    LQGVIFDLDGVITDTAHLHFQAWQQIAAEIGISIDAQFNESLKGISRDESLRRILQHGGK 62
            LQ VIFDLDGVI DTA +H  AW+++A E G+  DA   E LKG+ R  SL  +L+  G+
Sbjct: 807  LQAVIFDLDGVIADTAVVHDAAWRRLAQETGLPFDASIGERLKGVDRMGSLDILLERAGR 866

Query: 63   EGDFNSQERAQLAYRKNLLYVHSLRELTVNAVLPGIRSLLADLRAQQISVGLASVSLNAP 122
               ++++E+  L  RKN  Y   ++    + +LPG R+ +A +RA  + VGLAS S NAP
Sbjct: 867  A--YSAEEKLALGERKNDYYREQIQRFGPDQLLPGARAAIAAVRAAGLKVGLASASRNAP 924

Query: 123  TILAALELREFFTFCADASQLKNSKPDPEIFLAACAGLGVPPQACIGIEDAQAGIDAINA 182
             +L  L +   F +  DA+ ++ SKPDPEIFLAA AGLGV P AC+G+EDA AG+ +I+A
Sbjct: 925  LLLERLGVAHLFDYIVDAAHIQRSKPDPEIFLAAAAGLGVAPAACLGVEDAAAGVASIHA 984

Query: 183  SGMRSVGIG--AGLTGAQLLLP 202
            +GM +VGIG  + L  A+ +LP
Sbjct: 985  AGMAAVGIGQPSALAQAETVLP 1006


Lambda     K      H
   0.320    0.135    0.392 

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: 573
Number of extensions: 27
Number of successful extensions: 2
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: 219
Length of database: 1036
Length adjustment: 33
Effective length of query: 186
Effective length of database: 1003
Effective search space:   186558
Effective search space used:   186558
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: 51 (24.3 bits)

Align candidate N515DRAFT_1906 N515DRAFT_1906 (alpha,alpha-trehalose phosphorylase)
to HMM TIGR01990 (pgmB: beta-phosphoglucomutase (EC 5.4.2.6))

# 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/TIGR01990.hmm
# target sequence database:        /tmp/gapView.14578.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01990  [M=187]
Accession:   TIGR01990
Description: bPGM: beta-phosphoglucomutase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    1.5e-72  229.6   0.0    1.2e-71  226.6   0.0    2.1  2  lcl|FitnessBrowser__Dyella79:N515DRAFT_1906  N515DRAFT_1906 alpha,alpha-treha


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_1906  N515DRAFT_1906 alpha,alpha-trehalose phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0     0.028     0.028      10      45 ..     668     703 ..     666     708 .. 0.92
   2 !  226.6   0.0   1.2e-71   1.2e-71       1     187 []     807     993 ..     807     993 .. 0.99

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.028
                                    TIGR01990  10 GvitdtaeyhylawkkladelgiefdeelnesLkGv 45 
                                                  Gvi+  + +  +aw+   d+l + +d +  ++ +Gv
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1906 668 GVIAAEVGLAAKAWRYFQDSLRVDLDDSHGNAAHGV 703
                                                  999999********************9999998888 PP

  == domain 2  score: 226.6 bits;  conditional E-value: 1.2e-71
                                    TIGR01990   1 lkaviFDlDGvitdtaeyhylawkkladelgiefdeelnesLkGvsReesleailkkakkkyseee 66 
                                                  l+aviFDlDGvi+dta  h  aw++la+e g++fd ++ e+LkGv R+ sl+++l++a+++ys+ee
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1906 807 LQAVIFDLDGVIADTAVVHDAAWRRLAQETGLPFDASIGERLKGVDRMGSLDILLERAGRAYSAEE 872
                                                  58**************************************************************** PP

                                    TIGR01990  67 keelaerknekYvellkeltpedvlpgikelleelkkkkikialasasknaklvleklelkdkfda 132
                                                  k +l erkn++Y+e ++ + p+++lpg ++ ++ ++++++k++lasas+na+l+le+l++++ fd+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1906 873 KLALGERKNDYYREQIQRFGPDQLLPGARAAIAAVRAAGLKVGLASASRNAPLLLERLGVAHLFDY 938
                                                  ****************************************************************** PP

                                    TIGR01990 133 ivdaaevkkgkPdPeiFlaaaeklgvspeecigieDaeaGieaikaagilavgvg 187
                                                  ivdaa+++++kPdPeiFlaaa+ lgv+p++c+g+eDa+aG+ +i+aag+ avg+g
  lcl|FitnessBrowser__Dyella79:N515DRAFT_1906 939 IVDAAHIQRSKPDPEIFLAAAAGLGVAPAACLGVEDAAAGVASIHAAGMAAVGIG 993
                                                  *****************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (187 nodes)
Target sequences:                          1  (1036 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: 29.75
//
[ok]

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources