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.24779.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 9.64
//
[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:

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