Alignments for a candidate for glk in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Pseudomonas putida KT2440

Align Glucokinase (EC 2.7.1.2) (characterized)
to candidate PP_1011 PP_1011 glucokinase

Query= reanno::WCS417:GFF4431
         (318 letters)



>FitnessBrowser__Putida:PP_1011
          Length = 319

 Score =  449 bits (1156), Expect = e-131
 Identities = 218/316 (68%), Positives = 258/316 (81%)

Query: 1   MKLALVGDIGGTNARFALWRDQELHSIRVHATADHSSPEDAIKVYLKEEGLEIGDIGAVC 60
           MK  LVGDIGGTNARFALWRD +LH + V AT D+++PE AI+ YL+ +G+  G + AVC
Sbjct: 1   MKHLLVGDIGGTNARFALWRDNQLHEVNVFATVDYTNPEQAIEAYLESQGIARGGLAAVC 60

Query: 61  LSVAGPVSGDEFKFTNNHWRLSKTAFCKTLQVDELLLVNDFSAMALGMTRLKPDEFRVVC 120
           L+VAGPV GDEF+FTNNHWRLS+TAFCKTLQV+ LLL+NDF+AMALGMTRL+  EFR VC
Sbjct: 61  LAVAGPVDGDEFRFTNNHWRLSRTAFCKTLQVERLLLINDFTAMALGMTRLREGEFREVC 120

Query: 121 EGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHIYT 180
            G  +P RPA+VIGPGTGLGVG+LL LG   + ALPGEGGHVDLP+ + RE  + Q I++
Sbjct: 121 PGQADPSRPALVIGPGTGLGVGSLLRLGEQLWKALPGEGGHVDLPVGNAREAAIHQQIHS 180

Query: 181 EIGHVSAETALSGGGLPRLYRAICAVDGHTPVLETPEAITAAGLAGDPVAMEVLDQFSIW 240
           +IGHVSAE  LSGGGL RLY+AICA+DG TP  +TP  IT A L G+P A+ V++QF  +
Sbjct: 181 QIGHVSAEAVLSGGGLVRLYQAICALDGDTPRHKTPAHITDAALGGEPRALAVVEQFCRF 240

Query: 241 LGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFINSGFAKSFADKGCMSDYFKGIPVWLVT 300
           LGRVAGNNVLT G RGGVYIVGGVIPRFA+ F+ SGFA SFADKGCMS YF G+PVWLVT
Sbjct: 241 LGRVAGNNVLTLGARGGVYIVGGVIPRFAELFLRSGFAASFADKGCMSGYFTGVPVWLVT 300

Query: 301 APYSGLTGAGVALEQA 316
           A +SGL GAGVAL+QA
Sbjct: 301 AEFSGLEGAGVALQQA 316


Lambda     K      H
   0.320    0.139    0.429 

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: 388
Number of extensions: 12
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: 318
Length of database: 319
Length adjustment: 27
Effective length of query: 291
Effective length of database: 292
Effective search space:    84972
Effective search space used:    84972
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: 48 (23.1 bits)

Align candidate PP_1011 PP_1011 (glucokinase)
to HMM TIGR00749 (glk: glucokinase (EC 2.7.1.2))

# 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/TIGR00749.hmm
# target sequence database:        /tmp/gapView.30155.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00749  [M=315]
Accession:   TIGR00749
Description: glk: glucokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    4.6e-82  261.8   0.0    5.3e-82  261.5   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_1011  PP_1011 glucokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_1011  PP_1011 glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.5   0.0   5.3e-82   5.3e-82       1     315 []       5     310 ..       5     310 .. 0.97

  Alignments for each domain:
  == domain 1  score: 261.5 bits;  conditional E-value: 5.3e-82
                           TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvrltnl 75 
                                         lvgdiGGtnar+al      +++ v+++ + d+ + e+++  yle + +  +     c+a+a+P+ gd  r+tn+
  lcl|FitnessBrowser__Putida:PP_1011   5 LVGDIGGTNARFAL--WRDNQLHEVNVFATVDYTNPEQAIEAYLESQGIARGGLAAVCLAVAGPVDGDEFRFTNN 77 
                                         89************..8899****************************999998899****************** PP

                           TIGR00749  76 dWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliqqsdgry 150
                                         +W ls     ++l +++l lindf+a+a++++ l+e ++  +   ++++s +  ++G+GtGlGv  l++ +++ +
  lcl|FitnessBrowser__Putida:PP_1011  78 HWRLSRTAFCKTLQVERLLLINDFTAMALGMTRLREGEFREVCPGQADPSRPALVIGPGTGLGVGSLLRLGEQLW 152
                                         *************************************************************************** PP

                           TIGR00749 151 kvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeelkekdise 225
                                         k+l+geGghvd+   +  e+ + + +++++g+vsae vlsG Glv +y+a+   +g+      +  ++++  i++
  lcl|FitnessBrowser__Putida:PP_1011 153 KALPGEGGHVDLPVGNAREAAIHQQIHSQIGHVSAEAVLSGGGLVRLYQAICALDGDT-----P-RHKTPAHITD 221
                                         *****************************************************99654.....3.456899**** PP

                           TIGR00749 226 aalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrlkellasiP 300
                                         aal g+ + a   +e f+  lG++agn  l+lgarGGvy++GG++Prf el+ +s+f a+f dkG +  +++ +P
  lcl|FitnessBrowser__Putida:PP_1011 222 AALGGE-PRALAVVEQFCRFLGRVAGNNVLTLGARGGVYIVGGVIPRFAELFLRSGFAASFADKGCMSGYFTGVP 295
                                         ***875.788899************************************************************** PP

                           TIGR00749 301 vqvvlkkkvGllGag 315
                                         v +v  +  Gl Gag
  lcl|FitnessBrowser__Putida:PP_1011 296 VWLVTAEFSGLEGAG 310
                                         *************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (319 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.28
//
[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