Alignments for a candidate for glk in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Sinorhizobium meliloti 1021

Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate SMc02835 SMc02835 glucokinase

Query= curated2:B9JYQ5
         (340 letters)



>FitnessBrowser__Smeli:SMc02835
          Length = 339

 Score =  457 bits (1177), Expect = e-133
 Identities = 225/338 (66%), Positives = 268/338 (79%), Gaps = 1/338 (0%)

Query: 4   PHDNDH-MPFPVLVGDIGGTNARFWILMDAHAAPKEFANIHTADFPTIDQAIQDCILDKS 62
           P+ ++H  PFP+L+GDIGGTNARF +L DA+  PK+ A I T DF TI++A+Q  ILDK+
Sbjct: 2   PNASEHSFPFPILIGDIGGTNARFALLTDAYGEPKQLAPIRTGDFATIEEAMQKGILDKT 61

Query: 63  GFQPRSAILAVAGPIKDDEIPLTNCPWVIRPKAMIADLGFDDVLVVNDFEAQALAAASLG 122
             QPRSAILAVAGPIK DEIPLTN  WVIRPK M+A LG +DVLV+NDFEAQALA A+  
Sbjct: 62  SVQPRSAILAVAGPIKGDEIPLTNAGWVIRPKDMLAGLGLEDVLVINDFEAQALAIAAPA 121

Query: 123 RNDREPIGPLTETSLNSRVILGPGTGLGVGGLLYTHHTWFPVPGEGGHVDIGPRSDRDWQ 182
             D   IG       +SRV+LGPGTGLGV GL+Y  HTW PVPGEGGHVDIGPR++RD++
Sbjct: 122 DQDVVQIGGGAVRPFHSRVVLGPGTGLGVAGLVYAQHTWIPVPGEGGHVDIGPRTERDFR 181

Query: 183 IFPHIERIEGRISGEQILCGRGILHLYNAICAADGIEPVWTDPADVTQHALKGNDPVCVE 242
           I+P +E IEGR++GEQILCGRGI++LY A+CAA+G E V  D A VT  AL G D   VE
Sbjct: 182 IWPFLEPIEGRMAGEQILCGRGIMNLYRAVCAANGEEAVLADQAAVTTSALSGADAAAVE 241

Query: 243 TMTLFVTYLGRIAGDMALVFMARGGVFLSGGISQKIIPLLKSPVFRAAFEDKAPHTEMMK 302
           T++LF TYLGR+AGDMAL+FMARGGVFL+GGISQKI+P L  P FRAAFEDKAPH+ +M+
Sbjct: 242 TVSLFATYLGRVAGDMALIFMARGGVFLAGGISQKILPALTKPEFRAAFEDKAPHSALMR 301

Query: 303 TIPTFVAIHPQAALSGLAAYARTPSSYGVKHEGRRWQR 340
           TIPTF  IHP AALSGLAA+ARTP  +GV  EGRRW+R
Sbjct: 302 TIPTFAVIHPMAALSGLAAFARTPRDFGVAMEGRRWRR 339


Lambda     K      H
   0.322    0.140    0.445 

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: 440
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: 340
Length of database: 339
Length adjustment: 28
Effective length of query: 312
Effective length of database: 311
Effective search space:    97032
Effective search space used:    97032
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: 49 (23.5 bits)

Align candidate SMc02835 SMc02835 (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.2446.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
    3.4e-73  232.6   0.1    4.1e-73  232.3   0.1    1.0  1  lcl|FitnessBrowser__Smeli:SMc02835  SMc02835 glucokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc02835  SMc02835 glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.3   0.1   4.1e-73   4.1e-73       1     313 [.      14     317 ..      14     319 .. 0.95

  Alignments for each domain:
  == domain 1  score: 232.3 bits;  conditional E-value: 4.1e-73
                           TIGR00749   1 lvgdiGGtnarlalvevapgeieqvktyssedfpsleavvrv.yleeakvelkdpikgcfaiatPiigdfvrltn 74 
                                         l+gdiGGtnar+al+  a ge +q+   ++ df  +e++++   l+++ v+   p  + +a+a+Pi gd + ltn
  lcl|FitnessBrowser__Smeli:SMc02835  14 LIGDIGGTNARFALLTDAYGEPKQLAPIRTGDFATIEEAMQKgILDKTSVQ---PRSAILAVAGPIKGDEIPLTN 85 
                                         79**********************************999987255655554...5679***************** PP

                           TIGR00749  75 ldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGvatliqqsdgr 149
                                           W +  +++   l+l+ + +indf a+a+ai+a  ++d++q+gg  v +  +  +lG+GtGlGva l+  ++  
  lcl|FitnessBrowser__Smeli:SMc02835  86 AGWVIRPKDMLAGLGLEDVLVINDFEAQALAIAAPADQDVVQIGGGAVRPFHSRVVLGPGTGLGVAGLVY-AQHT 159
                                         *********************************************************************9.9*** PP

                           TIGR00749 150 ykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgerevsklskeelkekdis 224
                                         +  ++geGghvd  Pr e ++ ++ +l    gr++ e++l G G++++y+a+  ++ge+ v  l      +  ++
  lcl|FitnessBrowser__Smeli:SMc02835 160 WIPVPGEGGHVDIGPRTERDFRIWPFLEPIEGRMAGEQILCGRGIMNLYRAVCAANGEEAV--LA----DQAAVT 228
                                         *****************************99*************************98865..44....45679* PP

                           TIGR00749 225 eaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrlkellasi 299
                                          +al g d+ a ++++lf + lG++ag++al + arGGv++aGGi  ++++ l k  fraafedk    +l+ +i
  lcl|FitnessBrowser__Smeli:SMc02835 229 TSALSGADAAAVETVSLFATYLGRVAGDMALIFMARGGVFLAGGISQKILPALTKPEFRAAFEDKAPHSALMRTI 303
                                         *************************************************************************** PP

                           TIGR00749 300 PvqvvlkkkvGllG 313
                                         P   v++  + l G
  lcl|FitnessBrowser__Smeli:SMc02835 304 PTFAVIHPMAALSG 317
                                         *******9998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (339 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: 8.35
//
[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