Alignments for a candidate for glk in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Pseudomonas fluorescens FW300-N2E3

Align Glucokinase (EC 2.7.1.2) (characterized)
to candidate AO353_03415 AO353_03415 glucokinase

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



>FitnessBrowser__pseudo3_N2E3:AO353_03415
          Length = 316

 Score =  566 bits (1459), Expect = e-166
 Identities = 276/316 (87%), Positives = 295/316 (93%)

Query: 1   MKLALVGDIGGTNARFALWRDQELHSIRVHATADHSSPEDAIKVYLKEEGLEIGDIGAVC 60
           +KLALVGDIGGTNARFALW+DQ+L SI+V ATAD++ PEDAI VYL   GL  G IGAVC
Sbjct: 1   VKLALVGDIGGTNARFALWKDQQLESIQVLATADYACPEDAIGVYLSGLGLAPGSIGAVC 60

Query: 61  LSVAGPVSGDEFKFTNNHWRLSKTAFCKTLQVDELLLVNDFSAMALGMTRLKPDEFRVVC 120
           LSVAGPVSGDEF+FTNNHWRLS+ AFC+TLQVD LLLVNDFSAMALGMTRL+P EFRVVC
Sbjct: 61  LSVAGPVSGDEFRFTNNHWRLSRKAFCQTLQVDRLLLVNDFSAMALGMTRLQPGEFRVVC 120

Query: 121 EGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHIYT 180
           EGTPEPLRPAVVIGPGTGLGVGTLLDLG GR+AALPGEGGHVDLPLSSPRETQLWQHIY 
Sbjct: 121 EGTPEPLRPAVVIGPGTGLGVGTLLDLGEGRWAALPGEGGHVDLPLSSPRETQLWQHIYN 180

Query: 181 EIGHVSAETALSGGGLPRLYRAICAVDGHTPVLETPEAITAAGLAGDPVAMEVLDQFSIW 240
           EIGHVSAETALSGGGLPR+YRAICAVDGH PVL+TPEAITAAGLAGDP+A+EVL+QF  W
Sbjct: 181 EIGHVSAETALSGGGLPRVYRAICAVDGHEPVLDTPEAITAAGLAGDPIAVEVLEQFCCW 240

Query: 241 LGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFINSGFAKSFADKGCMSDYFKGIPVWLVT 300
           LGRVAGNNVLT GGRGGVYIVGGVIPRFADFF+ SGFA+ FADKGCMS+YFKGIPVWLVT
Sbjct: 241 LGRVAGNNVLTVGGRGGVYIVGGVIPRFADFFLKSGFARCFADKGCMSEYFKGIPVWLVT 300

Query: 301 APYSGLTGAGVALEQA 316
           APYSGLTGAGVALEQA
Sbjct: 301 APYSGLTGAGVALEQA 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: 450
Number of extensions: 7
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: 316
Length adjustment: 27
Effective length of query: 291
Effective length of database: 289
Effective search space:    84099
Effective search space used:    84099
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 AO353_03415 AO353_03415 (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.28454.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
    4.4e-82  261.8   0.0    5.1e-82  261.6   0.0    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03415  AO353_03415 glucokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_03415  AO353_03415 glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.6   0.0   5.1e-82   5.1e-82       1     315 []       5     310 ..       5     310 .. 0.97

  Alignments for each domain:
  == domain 1  score: 261.6 bits;  conditional E-value: 5.1e-82
                                     TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpi.kgcfaiatP 64 
                                                   lvgdiGGtnar+al     +++e+++++ + d+   e+++ vyl+      +  i   c+++a+P
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03415   5 LVGDIGGTNARFAL--WKDQQLESIQVLATADYACPEDAIGVYLSGLGLAPGS-IgAVCLSVAGP 66 
                                                   89************..8899**************************9999998.5489******* PP

                                     TIGR00749  65 iigdfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaia 129
                                                   + gd  r+tn++W ls +   q+l + +l l+ndf+a+a++++ l+  ++ ++    +e+  +  
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03415  67 VSGDEFRFTNNHWRLSRKAFCQTLQVDRLLLVNDFSAMALGMTRLQPGEFRVVCEGTPEPLRPAV 131
                                                   ***************************************************************** PP

                                     TIGR00749 130 ilGaGtGlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGl 194
                                                   ++G+GtGlGv tl++ ++gr+ +l+geGghvd+   s+ e++l++ + +++g+vsae  lsG Gl
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03415 132 VIGPGTGLGVGTLLDLGEGRWAALPGEGGHVDLPLSSPRETQLWQHIYNEIGHVSAETALSGGGL 196
                                                   ***************************************************************** PP

                                     TIGR00749 195 vliyealskrkgerevsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklga 259
                                                     +y+a+   +g++ v  l     +++ i+ a l+g+ ++a + le f+  lG++agn  l++g 
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03415 197 PRVYRAICAVDGHEPV--L----DTPEAITAAGLAGD-PIAVEVLEQFCCWLGRVAGNNVLTVGG 254
                                                   ***********88866..4....4899********96.78999********************** PP

                                     TIGR00749 260 rGGvyvaGGivPrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315
                                                   rGGvy++GG++Prf +++ ks+f   f dkG + e+++ iPv +v     Gl Gag
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_03415 255 RGGVYIVGGVIPRFADFFLKSGFARCFADKGCMSEYFKGIPVWLVTAPYSGLTGAG 310
                                                   ******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (316 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: 00:00:00.00
# Mc/sec: 10.37
//
[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