Alignments for a candidate for glk in Methylococcus capsulatus Bath

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Methylococcus capsulatus Bath

Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_010959909.1 MCA_RS02785 glucokinase

Query= curated2:B2J224
         (341 letters)



>NCBI__GCF_000008325.1:WP_010959909.1
          Length = 330

 Score =  224 bits (570), Expect = 3e-63
 Identities = 134/351 (38%), Positives = 188/351 (53%), Gaps = 34/351 (9%)

Query: 3   LLLAGDIGGTKTILQLVETSDSQGLHTIYQESYHSADFPDLVPIVQQFLIKANTPIPEKA 62
           +LLAGD+G TKT+L L +    + L ++ +  + S D+  L  +V  FL       PE A
Sbjct: 1   MLLAGDVGATKTVLGLFDCWGDR-LVSLSEAIFASTDYASLETVVAAFLDGQEERRPEVA 59

Query: 63  CFAIAGPIVKNTAKLTNLAWFLDTERLQQELGIPHIYLINDFAAVGYGIS-GLQKQDLHP 121
           CF + GP+ +   ++TNL W L    L    G+  + L+ND  A+  G++  L + D   
Sbjct: 60  CFGVPGPVSEGRCEITNLPWVLSERELAAATGVSAVRLLNDVQAMALGMAYRLGEDDWVE 119

Query: 122 LQVGKPQPETP-IGIIGAGTGLGQGFLIKQGNNYQVFPSEGGHADFAPRNEIEFQLLKYL 180
           L  G  +P +  + +I AGTGLG+  L   G  Y   P+EGGH+DFAP   +E  LL +L
Sbjct: 120 LNPGAGRPRSGNVAVIAAGTGLGEAILYWDGERYHALPTEGGHSDFAPNGPLEEGLLAFL 179

Query: 181 LDKHDIQRISVERVVSGMGIVAIYQFLRDRKFAAES----------PDIAQIVRTWEQEA 230
            D+     +S ER++SG G+  +Y +LR    A ES          PD A I+  W    
Sbjct: 180 RDRF-CGHVSYERILSGSGLANLYDYLRHAGVAPESEALHAALASAPDRAPIIAEW---- 234

Query: 231 GQEEKSVDPGAAIGTAALEKRDRLSEQTLQLFIEAYGAEAGNLALKLLPYGGLYIAGGIA 290
                           ALE+RD L    L LF   YGAEAGNLALK L  GG+ + GGIA
Sbjct: 235 ----------------ALERRDALCTAVLDLFAAIYGAEAGNLALKSLALGGVILGGGIA 278

Query: 291 PKILPLIQNSGFLLNFTQKGRMRPLLEEIPVYIILNPQVGLIGAALCAARL 341
           PKILP++Q   F+  FT KGR+ PLL  +PV + ++PQ  L+GAA  A+ +
Sbjct: 279 PKILPVLQAGRFMAAFTAKGRLSPLLGRLPVRVAIHPQPALLGAAHAASAM 329


Lambda     K      H
   0.320    0.140    0.408 

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: 291
Number of extensions: 11
Number of successful extensions: 5
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: 341
Length of database: 330
Length adjustment: 28
Effective length of query: 313
Effective length of database: 302
Effective search space:    94526
Effective search space used:    94526
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: 49 (23.5 bits)

Align candidate WP_010959909.1 MCA_RS02785 (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.2098.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    1.6e-81  260.0   0.0    1.8e-81  259.8   0.0    1.0  1  lcl|NCBI__GCF_000008325.1:WP_010959909.1  MCA_RS02785 glucokinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000008325.1:WP_010959909.1  MCA_RS02785 glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  259.8   0.0   1.8e-81   1.8e-81       1     315 []       3     323 ..       3     323 .. 0.93

  Alignments for each domain:
  == domain 1  score: 259.8 bits;  conditional E-value: 1.8e-81
                                 TIGR00749   1 lvgdiGGtnarlalvevapgeieqv..ktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiig 67 
                                               l+gd+G t+++l+l +    ++ ++   ++ s+d+ sle vv  +l+ +++    p  +cf + +P+ +
  lcl|NCBI__GCF_000008325.1:WP_010959909.1   3 LAGDVGATKTVLGLFDCWGDRLVSLseAIFASTDYASLETVVAAFLDGQEER--RPEVACFGVPGPVSE 69 
                                               79*************986655444446789****************998775..5669*********** PP

                                 TIGR00749  68 dfvrltnldWalsieelkqelalaklelindfaavayail.alkeedliqlg.gakveesaaiailGaG 134
                                                 +++tnl W ls  el+   +++ + l+nd  a+a++++  l+e+d + l+ ga    s+ +a++ aG
  lcl|NCBI__GCF_000008325.1:WP_010959909.1  70 GRCEITNLPWVLSERELAAATGVSAVRLLNDVQAMALGMAyRLGEDDWVELNpGAGRPRSGNVAVIAAG 138
                                               *************************************996369*******9757888899********* PP

                                 TIGR00749 135 tGlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkky.grvsaervlsGsGlvliyeals 202
                                               tGlG a l  +  +ry++l++eGgh dfaP+ +le  ll +lr ++ g+vs er+lsGsGl+++y++l+
  lcl|NCBI__GCF_000008325.1:WP_010959909.1 139 TGLGEAILYWD-GERYHALPTEGGHSDFAPNGPLEEGLLAFLRDRFcGHVSYERILSGSGLANLYDYLR 206
                                               ******99994.579****************************************************** PP

                                 TIGR00749 203 krkgere....vsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaG 267
                                               ++    e     + l  +  +  +i+e ale  d+l+   l+lf +i+Ga+agnlalk +a GGv + G
  lcl|NCBI__GCF_000008325.1:WP_010959909.1 207 HAGVAPEsealHAALASAPDRAPIIAEWALERRDALCTAVLDLFAAIYGAEAGNLALKSLALGGVILGG 275
                                               *96444433777889999999999********************************************* PP

                                 TIGR00749 268 GivPrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315
                                               Gi+P++++ l+++ f+aaf  kGrl  ll+ +Pv+v ++ ++ llGa+
  lcl|NCBI__GCF_000008325.1:WP_010959909.1 276 GIAPKILPVLQAGRFMAAFTAKGRLSPLLGRLPVRVAIHPQPALLGAA 323
                                               **********************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (330 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.60
//
[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:

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