GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Pseudomonas fluorescens FW300-N2C3

Align Glucokinase (EC 2.7.1.2) (characterized)
to candidate AO356_05215 AO356_05215 glucokinase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_05215
          Length = 318

 Score =  555 bits (1430), Expect = e-163
 Identities = 268/318 (84%), Positives = 294/318 (92%)

Query: 1   MKLALVGDIGGTNARFALWRDQELHSIRVHATADHSSPEDAIKVYLKEEGLEIGDIGAVC 60
           +KLALVGDIGGTNARFALW+D  L +I+V ATAD++ PEDAI+VYL   GL+ G IG+VC
Sbjct: 1   LKLALVGDIGGTNARFALWKDHTLENIQVLATADYACPEDAIQVYLGGLGLKPGAIGSVC 60

Query: 61  LSVAGPVSGDEFKFTNNHWRLSKTAFCKTLQVDELLLVNDFSAMALGMTRLKPDEFRVVC 120
           LSVAGPVSGDEF+FTNNHWRLS  AFCKTLQV++LLLVNDFSAMALGMT L+PDE+RVVC
Sbjct: 61  LSVAGPVSGDEFRFTNNHWRLSNLAFCKTLQVEKLLLVNDFSAMALGMTCLRPDEYRVVC 120

Query: 121 EGTPEPLRPAVVIGPGTGLGVGTLLDLGAGRFAALPGEGGHVDLPLSSPRETQLWQHIYT 180
           EGTPEP+RPAVVIGPGTGLGVGTLLDLG GRFAALPGEGGHVDLP+SSPRETQLWQHIY 
Sbjct: 121 EGTPEPMRPAVVIGPGTGLGVGTLLDLGEGRFAALPGEGGHVDLPMSSPRETQLWQHIYN 180

Query: 181 EIGHVSAETALSGGGLPRLYRAICAVDGHTPVLETPEAITAAGLAGDPVAMEVLDQFSIW 240
           EIGHVSAETALSG GLPR+YRAICAVDGH PVL+TPE+ITAAGLAGDP+A+EVL+QF  W
Sbjct: 181 EIGHVSAETALSGSGLPRVYRAICAVDGHVPVLDTPESITAAGLAGDPIALEVLEQFCRW 240

Query: 241 LGRVAGNNVLTTGGRGGVYIVGGVIPRFADFFINSGFAKSFADKGCMSDYFKGIPVWLVT 300
           LGRVAGNNVLT GGRGGVYIVGGV+PRFADFF+ SGFA+ FADKGCMSDYFKGIPVWLVT
Sbjct: 241 LGRVAGNNVLTLGGRGGVYIVGGVVPRFADFFLESGFARCFADKGCMSDYFKGIPVWLVT 300

Query: 301 APYSGLTGAGVALEQAFA 318
           APYSGL GAGVALEQ+ A
Sbjct: 301 APYSGLMGAGVALEQSAA 318


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: 465
Number of extensions: 11
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: 318
Length adjustment: 27
Effective length of query: 291
Effective length of database: 291
Effective search space:    84681
Effective search space used:    84681
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 AO356_05215 AO356_05215 (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.9947.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
    4.7e-82  261.7   0.0    5.4e-82  261.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05215  AO356_05215 glucokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05215  AO356_05215 glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  261.5   0.0   5.4e-82   5.4e-82       1     315 []       5     310 ..       5     310 .. 0.96

  Alignments for each domain:
  == domain 1  score: 261.5 bits;  conditional E-value: 5.4e-82
                                       TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpi.kgcfaia 62 
                                                     lvgdiGGtnar+al       +e+++++ + d+   e++++vyl     + +  i   c+++a
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05215   5 LVGDIGGTNARFAL--WKDHTLENIQVLATADYACPEDAIQVYLGGLGLKPGA-IgSVCLSVA 64 
                                                     89************..78899***********************999888887.5599***** PP

                                       TIGR00749  63 tPiigdfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakvees 125
                                                     +P+ gd  r+tn++W ls     ++l ++kl l+ndf+a+a++++ l+ ++  ++    +e+ 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05215  65 GPVSGDEFRFTNNHWRLSNLAFCKTLQVEKLLLVNDFSAMALGMTCLRPDEYRVVCEGTPEPM 127
                                                     *************************************************************** PP

                                       TIGR00749 126 aaiailGaGtGlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaerv 188
                                                      +  ++G+GtGlGv tl++ ++gr+ +l+geGghvd+   s+ e++l++ + +++g+vsae  
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05215 128 RPAVVIGPGTGLGVGTLLDLGEGRFAALPGEGGHVDLPMSSPRETQLWQHIYNEIGHVSAETA 190
                                                     *************************************************************** PP

                                       TIGR00749 189 lsGsGlvliyealskrkgerevsklskeelkekdiseaalegsdvlarralelflsilGalag 251
                                                     lsGsGl  +y+a+   +g  +v  l     +++ i+ a l+g+ ++a + le f+  lG++ag
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05215 191 LSGSGLPRVYRAICAVDG--HVPVLD----TPESITAAGLAGD-PIALEVLEQFCRWLGRVAG 246
                                                     ***************994..344455....99*********96.89999************** PP

                                       TIGR00749 252 nlalklgarGGvyvaGGivPrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGa 314
                                                     n  l+lg rGGvy++GG+vPrf +++ +s+f   f dkG + ++++ iPv +v     Gl+Ga
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05215 247 NNVLTLGGRGGVYIVGGVVPRFADFFLESGFARCFADKGCMSDYFKGIPVWLVTAPYSGLMGA 309
                                                     **************************************************************9 PP

                                       TIGR00749 315 g 315
                                                     g
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_05215 310 G 310
                                                     7 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (318 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: 00:00:00.01
# Mc/sec: 7.30
//
[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