GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Neiella marina J221

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate WP_087504727.1 CBE68_RS03760 glucokinase

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



>NCBI__GCF_002165625.1:WP_087504727.1
          Length = 320

 Score =  305 bits (782), Expect = 7e-88
 Identities = 153/310 (49%), Positives = 199/310 (64%)

Query: 6   LVGDVGGTNARLALCDIASGEISQAKTYSGLDYPSLEAVIRVYLEEHKVEVKDGCIAIAC 65
           L+ DVGGTN RLAL D    E ++ + Y    YP++  VIR YLEE    V+  CIAIAC
Sbjct: 7   LIADVGGTNIRLALVDEQGVEYTELRKYLCAQYPTITDVIRHYLEEVNASVRHACIAIAC 66

Query: 66  PITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEPV 125
           P   DW+ MTN++WAFS  E+++ LG   L IIND+TA+SM++P LK + ++Q G     
Sbjct: 67  PTNSDWIDMTNNSWAFSRREVQEELGLDALYIINDYTAISMSLPFLKDDQMVQVGPGMIE 126

Query: 126 EGKPIAVYGAGTGLGVAHLVHVDKRWVSLPGEGGHVDFAPNSEEEAIILEILRAEIGHVS 185
              P AV G GTGLGVAHLV V+  W SLPGEGGHVDFAP  + +  I + L     HVS
Sbjct: 127 PAAPKAVLGPGTGLGVAHLVSVEGHWHSLPGEGGHVDFAPIDDVDNYIWKYLNKRYPHVS 186

Query: 186 AERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIMGRFG 245
            E++LSG GL+ +Y A+ +          P DIT   +A  C  C+ A+  FC ++G   
Sbjct: 187 YEQLLSGLGLIQIYEALCEMRGVTVIERTPADITTLGVAGECELCQAAVEQFCKVLGSHA 246

Query: 246 GNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVHDNPG 305
           GNLA+NLG FGGV++AGGIVPRF +F + S FRA FE KGRF +YV  +P +LI  + PG
Sbjct: 247 GNLAMNLGAFGGVYVAGGIVPRFTDFVERSEFRARFEAKGRFTDYVRRVPTFLITEEQPG 306

Query: 306 LLGSGAHLRQ 315
           LLG+ A+L Q
Sbjct: 307 LLGAAAYLMQ 316


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: 325
Number of extensions: 13
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: 321
Length of database: 320
Length adjustment: 28
Effective length of query: 293
Effective length of database: 292
Effective search space:    85556
Effective search space used:    85556
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 WP_087504727.1 CBE68_RS03760 (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.3216528.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-108  349.2   0.0   1.3e-108  349.0   0.0    1.0  1  NCBI__GCF_002165625.1:WP_087504727.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002165625.1:WP_087504727.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  349.0   0.0  1.3e-108  1.3e-108       1     315 []       7     311 ..       7     311 .. 0.98

  Alignments for each domain:
  == domain 1  score: 349.0 bits;  conditional E-value: 1.3e-108
                             TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiigdfvrlt 73 
                                           l++d+GGtn rlalv+    e   ++ y + ++p +++v+r ylee + ++++   +c+aia+P   d++ +t
  NCBI__GCF_002165625.1:WP_087504727.1   7 LIADVGGTNIRLALVDEQGVEYTELRKYLCAQYPTITDVIRHYLEEVNASVRH---ACIAIACPTNSDWIDMT 76 
                                           79**************************************************9...***************** PP

                             TIGR00749  74 nldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliqqs 146
                                           n++Wa+s  e+++el+l  l +ind++a++++++ lk+++++q+g   +e++a++a+lG+GtGlGva+l+  +
  NCBI__GCF_002165625.1:WP_087504727.1  77 NNSWAFSRREVQEELGLDALYIINDYTAISMSLPFLKDDQMVQVGPGMIEPAAPKAVLGPGTGLGVAHLVS-V 148
                                           **********************************************************************9.* PP

                             TIGR00749 147 dgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeelk 219
                                           +g++++l+geGghvdfaP ++ +  +++yl k+y +vs e++lsG Gl++iyeal + +g          e +
  NCBI__GCF_002165625.1:WP_087504727.1 149 EGHWHSLPGEGGHVDFAPIDDVDNYIWKYLNKRYPHVSYEQLLSGLGLIQIYEALCEMRGVTV------IERT 215
                                           *******************************************************99985543......3568 PP

                             TIGR00749 220 ekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrl 292
                                           + di+   ++g++ l++ a+e f+ +lG+ agnla++lga+GGvyvaGGivPrf +++++s fra+fe kGr+
  NCBI__GCF_002165625.1:WP_087504727.1 216 PADITTLGVAGECELCQAAVEQFCKVLGSHAGNLAMNLGAFGGVYVAGGIVPRFTDFVERSEFRARFEAKGRF 288
                                           8************************************************************************ PP

                             TIGR00749 293 kellasiPvqvvlkkkvGllGag 315
                                            +++  +P  ++ ++++GllGa+
  NCBI__GCF_002165625.1:WP_087504727.1 289 TDYVRRVPTFLITEEQPGLLGAA 311
                                           *********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (320 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: 00:00:00.00
# Mc/sec: 13.49
//
[ok]

This GapMind analysis is from Sep 24 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