GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Caulobacter crescentus NA1000

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate CCNA_02133 CCNA_02133 glucokinase

Query= ecocyc::GLUCOKIN-MONOMER
         (321 letters)



>FitnessBrowser__Caulo:CCNA_02133
          Length = 331

 Score =  209 bits (533), Expect = 6e-59
 Identities = 125/313 (39%), Positives = 176/313 (56%), Gaps = 6/313 (1%)

Query: 6   LVGDVGGTNARLALCDIASGE--ISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKD-GCIA 62
           LVGD+GGTNAR AL +    +  + +   Y G DY + E  I  YL +  V+  D   +A
Sbjct: 11  LVGDIGGTNARFALVEFDGQDPRLIEPTAYRGEDYGTAEDAIEEYLRKVGVKHPDQAVVA 70

Query: 63  IACPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGA 122
           +A PI    V MTN  W  S   +++  GF + ++INDFTA ++A P +  + L Q G  
Sbjct: 71  VAGPIDHGQVHMTNLDWRISEDGLRRAGGFRNAKLINDFTAQALAAPRVGPKDLRQIGEL 130

Query: 123 EPVEGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEIL--RAE 180
                  +A+ G GTG GVA LV    + + L  EGGHV FAP  + E  +L  L  R +
Sbjct: 131 PTSGEGDLAILGPGTGFGVAGLVRRHGQEIPLATEGGHVAFAPVDDVEIEVLRALTRRLD 190

Query: 181 IGHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVI 240
            G VS ER+LSGPG+ +L+  +  A+ R  E L  K ITERA+ + C D    ++ FC I
Sbjct: 191 GGRVSVERILSGPGMEDLHVDLAAAEGRGVEALTAKQITERAV-EGCADSLATVNRFCAI 249

Query: 241 MGRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIV 300
           +G   G++AL LG  GGVFIAGGI PR ++  + S FR  F+ KGR   +   IP ++I+
Sbjct: 250 LGSTAGDIALTLGARGGVFIAGGIAPRIIDILEKSPFRERFDSKGRLSGFTRSIPTHVIL 309

Query: 301 HDNPGLLGSGAHL 313
           H +  L+G+   L
Sbjct: 310 HPHTALIGAAVAL 322


Lambda     K      H
   0.322    0.141    0.426 

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: 319
Number of extensions: 14
Number of successful extensions: 4
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: 321
Length of database: 331
Length adjustment: 28
Effective length of query: 293
Effective length of database: 303
Effective search space:    88779
Effective search space used:    88779
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate CCNA_02133 CCNA_02133 (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.2129219.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    3.1e-90  288.6   0.0    3.6e-90  288.4   0.0    1.0  1  lcl|FitnessBrowser__Caulo:CCNA_02133  CCNA_02133 glucokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Caulo:CCNA_02133  CCNA_02133 glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  288.4   0.0   3.6e-90   3.6e-90       1     315 []      11     319 ..      11     319 .. 0.95

  Alignments for each domain:
  == domain 1  score: 288.4 bits;  conditional E-value: 3.6e-90
                             TIGR00749   1 lvgdiGGtnarlalvevapgeieqv..ktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvr 71 
                                           lvgdiGGtnar+alve   ++ + +   +y++ed+   e+++  yl++  v +k+p ++ +a+a+Pi    v+
  lcl|FitnessBrowser__Caulo:CCNA_02133  11 LVGDIGGTNARFALVEFDGQDPRLIepTAYRGEDYGTAEDAIEEYLRK--VGVKHPDQAVVAVAGPIDHGQVH 81 
                                           89*************87766666665469*****************85..6789999**************** PP

                             TIGR00749  72 ltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliq 144
                                           +tnldW +s + l++  ++++ +lindf+a+a+a + ++ +dl q+g  ++  ++  ailG+GtG+Gva l++
  lcl|FitnessBrowser__Caulo:CCNA_02133  82 MTNLDWRISEDGLRRAGGFRNAKLINDFTAQALAAPRVGPKDLRQIGELPTSGEGDLAILGPGTGFGVAGLVR 154
                                           ************************************************************************9 PP

                             TIGR00749 145 qsdgrykvlageGghvdfaPrseleillleylrkky..grvsaervlsGsGlvliyealskrkgerevsklsk 215
                                             +g+   la+eGghv faP ++ ei +l+ l +++  grvs+er+lsG+G+  ++  l  ++g r v     
  lcl|FitnessBrowser__Caulo:CCNA_02133 155 -RHGQEIPLATEGGHVAFAPVDDVEIEVLRALTRRLdgGRVSVERILSGPGMEDLHVDLAAAEG-RGV----- 220
                                           .7899999************************999999*********************99993.334..... PP

                             TIGR00749 216 eelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafed 288
                                           e l+ k+i+e+a+eg ++++  +++ f++ilG+ ag++al+lgarGGv++aGGi+Pr+i++l+ks+fr++f+ 
  lcl|FitnessBrowser__Caulo:CCNA_02133 221 EALTAKQITERAVEG-CADSLATVNRFCAILGSTAGDIALTLGARGGVFIAGGIAPRIIDILEKSPFRERFDS 292
                                           566799*******98.778899*************************************************** PP

                             TIGR00749 289 kGrlkellasiPvqvvlkkkvGllGag 315
                                           kGrl  +  siP +v+l+ ++ l+Ga+
  lcl|FitnessBrowser__Caulo:CCNA_02133 293 KGRLSGFTRSIPTHVILHPHTALIGAA 319
                                           *************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (331 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 17.37
//
[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:

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