Alignments for a candidate for glk in Desulfotalea psychrophila LSv54

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Desulfotalea psychrophila LSv54

Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_011188303.1 DP_RS05330 glucokinase

Query= curated2:B2J224
         (341 letters)



>NCBI__GCF_000025945.1:WP_011188303.1
          Length = 332

 Score =  226 bits (576), Expect = 6e-64
 Identities = 137/338 (40%), Positives = 193/338 (57%), Gaps = 18/338 (5%)

Query: 3   LLLAGDIGGTKTILQLVETSDSQGLHTIYQES---YHSADFPDLVPIVQQFLIKANTPIP 59
           ++LAGDIGGTKT L L   S   G  ++   S   Y +ADF     +V  +L   +T I 
Sbjct: 1   MILAGDIGGTKTNLALYTCSCPAGNGSLIDSSAKTYLNADFASGEELVCGYLAGIDTTI- 59

Query: 60  EKACFAIAGPIVKNTAKLTNLAWFLDTERLQQELGIPHIYLINDFAAVGYGISGLQKQDL 119
           ++A FA+AGPI     K+TNL W +  E+L    GI  I+L+ND  A  Y +  L + +L
Sbjct: 60  KRAVFAVAGPIRDGQVKITNLPWLISVEQLSVATGIATIHLMNDLEATAYAVPFLSRDEL 119

Query: 120 HPLQVGKPQPETPIGIIGAGTGLGQGFLIKQGNNYQVFPSEGGHADFAPRNEIEFQLLKY 179
           + L  G       I +I  GTGLG+ FL  +G  Y    +EG H DFAP N ++ +LL Y
Sbjct: 120 YTLNQGISVERGNIALIAPGTGLGESFLTWEGTRYSAHATEGSHVDFAPTNALQIKLLDY 179

Query: 180 LLDKHDIQRISVERVVSGMGIVAIYQFLRDRKFAAESPDIAQIVRTWEQEAGQEEKSVDP 239
           LL     + +S ER+ SG+GI  IY FL+  +   E P+       W +E   +EK  D 
Sbjct: 180 LL--RGYEHVSYERICSGIGIPNIYGFLKHSQ-NIEEPE-------WLREQLSQEK--DH 227

Query: 240 GAAIGTAALEKRD--RLSEQTLQLFIEAYGAEAGNLALKLLPYGGLYIAGGIAPKILPLI 297
            A I  AAL+ +    +   T+++F+   GAEAGN+ALK++  GG+Y+ GGI P+IL L+
Sbjct: 228 TAVIVNAALDAQRPCPICRMTVEIFLSVLGAEAGNIALKVMAAGGVYVGGGIVPRILSLL 287

Query: 298 QNSGFLLNFTQKGRMRPLLEEIPVYIILNPQVGLIGAA 335
            N  F+  F  KGRM  LL ++PV+IILNP+V + GAA
Sbjct: 288 GNGLFMETFNSKGRMSELLVDVPVHIILNPKVAVFGAA 325


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: 281
Number of extensions: 17
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: 341
Length of database: 332
Length adjustment: 28
Effective length of query: 313
Effective length of database: 304
Effective search space:    95152
Effective search space used:    95152
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_011188303.1 DP_RS05330 (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.3023144.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.5e-87  279.8   0.1    1.7e-87  279.6   0.1    1.0  1  NCBI__GCF_000025945.1:WP_011188303.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000025945.1:WP_011188303.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.6   0.1   1.7e-87   1.7e-87       1     315 []       3     325 ..       3     325 .. 0.92

  Alignments for each domain:
  == domain 1  score: 279.6 bits;  conditional E-value: 1.7e-87
                             TIGR00749   1 lvgdiGGtnarlalv..evapgeieqv....ktyssedfpsleavvrvyleeakvelkdpikgcfaiatPiig 67 
                                           l+gdiGGt++ lal      +g+ + +    kty   df s e++v  yl    +++k    + fa+a+Pi +
  NCBI__GCF_000025945.1:WP_011188303.1   3 LAGDIGGTKTNLALYtcSCPAGNGSLIdssaKTYLNADFASGEELVCGYLAGIDTTIKR---AVFAVAGPIRD 72 
                                           79************74444445555445556***************************9...*********** PP

                             TIGR00749  68 dfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaaiailGaGtGlGva 140
                                             v++tnl W +s+e+l    ++a ++l+nd+ a aya++ l +++l  l+    +e + ia++ +GtGlG +
  NCBI__GCF_000025945.1:WP_011188303.1  73 GQVKITNLPWLISVEQLSVATGIATIHLMNDLEATAYAVPFLSRDELYTLNQGISVERGNIALIAPGTGLGES 145
                                           ***********************************************9997766777889************* PP

                             TIGR00749 141 tliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkgere.... 209
                                           +l      ry + a+eG+hvdfaP++ l+i ll+yl + y++vs er+ sG G+ +iy +l++ ++ +e    
  NCBI__GCF_000025945.1:WP_011188303.1 146 FLTW-EGTRYSAHATEGSHVDFAPTNALQIKLLDYLLRGYEHVSYERICSGIGIPNIYGFLKHSQNIEEpewl 217
                                           **99.6689********************************************************99996665 PP

                             TIGR00749 210 vsklskeelkekdiseaalegs..dvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiellkks 280
                                            ++ls+e+ +   i +aal+ +  ++++r ++e+fls+lGa+agn+alk+ a GGvyv GGivPr++ ll ++
  NCBI__GCF_000025945.1:WP_011188303.1 218 REQLSQEKDHTAVIVNAALDAQrpCPICRMTVEIFLSVLGAEAGNIALKVMAAGGVYVGGGIVPRILSLLGNG 290
                                           5667777777777******9764489*********************************************** PP

                             TIGR00749 281 sfraafedkGrlkellasiPvqvvlkkkvGllGag 315
                                            f+++f+ kGr+ ell ++Pv+++l+ kv + Ga+
  NCBI__GCF_000025945.1:WP_011188303.1 291 LFMETFNSKGRMSELLVDVPVHIILNPKVAVFGAA 325
                                           ********************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (332 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 23.89
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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