Alignments for a candidate for glk in Trichodesmium erythraeum IMS101

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Trichodesmium erythraeum IMS101

Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_011610590.1 TERY_RS03685 glucokinase

Query= curated2:B2J224
         (341 letters)



>NCBI__GCF_000014265.1:WP_011610590.1
          Length = 351

 Score =  430 bits (1106), Expect = e-125
 Identities = 221/351 (62%), Positives = 267/351 (76%), Gaps = 10/351 (2%)

Query: 1   MTLLLAGDIGGTKTILQLVETSDSQG-----LHTIYQESYHSADFPDLVPIVQQFLIKAN 55
           MTLL+AGDIGGTKTILQLVE +  +      L  +Y+  Y S DFPDLVPIV++FL +A+
Sbjct: 1   MTLLVAGDIGGTKTILQLVEVNREESKASVELRKLYENRYLSNDFPDLVPIVKKFLEEAS 60

Query: 56  TPI-----PEKACFAIAGPIVKNTAKLTNLAWFLDTERLQQELGIPHIYLINDFAAVGYG 110
             +     PEKACFAIAGP+V N  KLTNL W +D + ++ ELGI  I LINDF AVGYG
Sbjct: 61  EKLGEKQKPEKACFAIAGPVVNNIVKLTNLPWIIDAKLMENELGISQISLINDFEAVGYG 120

Query: 111 ISGLQKQDLHPLQVGKPQPETPIGIIGAGTGLGQGFLIKQGNNYQVFPSEGGHADFAPRN 170
           I GL  +DL  LQ G+P+ +TPI +IGAGTGLGQ FLI+     +V+P+EGGH DF  R+
Sbjct: 121 ILGLNTKDLETLQPGEPKSDTPIAVIGAGTGLGQCFLIRAAGVIKVYPTEGGHTDFKARS 180

Query: 171 EIEFQLLKYLLDKHDIQRISVERVVSGMGIVAIYQFLRDRKFAAESPDIAQIVRTWEQEA 230
           ++EF LLKYL   H+I+R+SVERVVSGMGIVAIYQFLRD  FA ESP+I   +R WE+E 
Sbjct: 181 QLEFDLLKYLKKLHNIKRVSVERVVSGMGIVAIYQFLRDSLFATESPEIGDQIRQWEKEV 240

Query: 231 GQEEKSVDPGAAIGTAALEKRDRLSEQTLQLFIEAYGAEAGNLALKLLPYGGLYIAGGIA 290
           G  + +VDPGA IG AALEK D L EQTL++FIEAYGAEAGNLALKLLPY GLYIAGGIA
Sbjct: 241 GSNQITVDPGAVIGKAALEKSDPLCEQTLKMFIEAYGAEAGNLALKLLPYSGLYIAGGIA 300

Query: 291 PKILPLIQNSGFLLNFTQKGRMRPLLEEIPVYIILNPQVGLIGAALCAARL 341
            KI+PLI +  F+  F  KGRM+PLLE+IPV++ILNP VGLIGAA+ A+ L
Sbjct: 301 AKIIPLINSGSFMEAFKDKGRMKPLLEKIPVHVILNPHVGLIGAAIRASNL 351


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: 382
Number of extensions: 12
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: 351
Length adjustment: 29
Effective length of query: 312
Effective length of database: 322
Effective search space:   100464
Effective search space used:   100464
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_011610590.1 TERY_RS03685 (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.26634.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-109  351.4   0.1   2.9e-109  351.1   0.1    1.0  1  lcl|NCBI__GCF_000014265.1:WP_011610590.1  TERY_RS03685 glucokinase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000014265.1:WP_011610590.1  TERY_RS03685 glucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.1   0.1  2.9e-109  2.9e-109       2     315 .]       6     345 ..       5     345 .. 0.92

  Alignments for each domain:
  == domain 1  score: 351.1 bits;  conditional E-value: 2.9e-109
                                 TIGR00749   2 vgdiGGtnarlalvevapgeieqv........ktyssedfpsleavvrvyleeakvelkd...pikgcf 59 
                                               +gdiGGt+++l lvev   e ++         + y s+dfp+l+++v+ +leea ++l++   p k+cf
  lcl|NCBI__GCF_000014265.1:WP_011610590.1   6 AGDIGGTKTILQLVEVNREESKASvelrklyeNRYLSNDFPDLVPIVKKFLEEASEKLGEkqkPEKACF 74 
                                               79************8776665544466666888999**********************8755677**** PP

                                 TIGR00749  60 aiatPiigdfvrltnldWalsieelkqelalaklelindfaavayailalkeedliqlggakveesaai 128
                                               aia+P+++++v+ltnl W +  + +++el+++++ lindf av+y+il+l+ +dl  l+  +++ +++i
  lcl|NCBI__GCF_000014265.1:WP_011610590.1  75 AIAGPVVNNIVKLTNLPWIIDAKLMENELGISQISLINDFEAVGYGILGLNTKDLETLQPGEPKSDTPI 143
                                               ********************************************************************* PP

                                 TIGR00749 129 ailGaGtGlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkky..grvsaervlsGsGlv 195
                                               a++GaGtGlG+++li+ + g  kv+++eGgh+df  rs+le+ ll+yl+k     rvs+erv+sG+G+v
  lcl|NCBI__GCF_000014265.1:WP_011610590.1 144 AVIGAGTGLGQCFLIR-AAGVIKVYPTEGGHTDFKARSQLEFDLLKYLKKLHniKRVSVERVVSGMGIV 211
                                               ***************9.99******************************865449************** PP

                                 TIGR00749 196 liyealskrkgere...vsklskeelkekd...........iseaalegsdvlarralelflsilGala 250
                                                iy++l+      e   +    +++ ke             i +aale sd+l++++l++f+ ++Ga+a
  lcl|NCBI__GCF_000014265.1:WP_011610590.1 212 AIYQFLRDSLFATEspeIGDQIRQWEKEVGsnqitvdpgavIGKAALEKSDPLCEQTLKMFIEAYGAEA 280
                                               *******987666544543334444444336666*********************************** PP

                                 TIGR00749 251 gnlalklgarGGvyvaGGivPrfiellkkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315
                                               gnlalkl+++ G+y+aGGi+ ++i+l++++sf++af+dkGr+k ll++iPv+v+l+ +vGl+Ga+
  lcl|NCBI__GCF_000014265.1:WP_011610590.1 281 GNLALKLLPYSGLYIAGGIAAKIIPLINSGSFMEAFKDKGRMKPLLEKIPVHVILNPHVGLIGAA 345
                                               ***************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (351 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: 00:00:00.00
# Mc/sec: 12.03
//
[ok]

This GapMind analysis is from Sep 24 2021. 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 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