Alignments for a candidate for glk in Leptospirillum ferrooxidans C2-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for glk in Leptospirillum ferrooxidans C2-3

Align Glucokinase; EC 2.7.1.2; Glucose kinase (uncharacterized)
to candidate WP_081495339.1 LFE_RS04280 glucokinase

Query= curated2:B2J224
         (341 letters)



>NCBI__GCF_000284315.1:WP_081495339.1
          Length = 400

 Score =  197 bits (501), Expect = 4e-55
 Identities = 120/348 (34%), Positives = 185/348 (53%), Gaps = 22/348 (6%)

Query: 3   LLLAGDIGGTKTIL---QLVETSDSQGLHTIYQESYHSADFPDLVPIVQQFLI-----KA 54
           L+L GDIGGTKT L    L E    +    +    Y S  +  L P++Q++L        
Sbjct: 55  LVLVGDIGGTKTSLALFSLAERGSREHFVPLCPAVYPSKRYDSLEPMIQEYLSWVRERLV 114

Query: 55  NTPIPEKACFAIAGPIVKNTAKLTNLAWFLDTERLQQELGIP--HIYLINDFAAVGYGIS 112
             P    A F +AGP+     + TNL W +D   L++ + +   ++ L+ND  A+ + + 
Sbjct: 115 GDPNIVAATFGVAGPVTGRVCRTTNLPWIVDAGSLEKLISVQEGNVNLLNDLEALAWSVG 174

Query: 113 GLQKQDLHPLQVGKPQPETPIGIIGAGTGLGQGFLIKQGNNYQVFPSEGGHADFAPRNEI 172
           G     L  +Q G+P   T + ++  GTGLG+  L  +  N+   PSEGGHAD+AP N+ 
Sbjct: 175 GDPLIPLATIQEGEPGTSTTMVLVAPGTGLGEAVLCGRDENFFALPSEGGHADWAPVNKE 234

Query: 173 EFQLLKYLLDKHDIQRISVERVVSGMGIVAIYQFLRDRKFAAESPDIAQIVRTWEQEAGQ 232
           + +LL+YL +  +   +SVERV+SGMGIV +Y FL     A   P              +
Sbjct: 235 QARLLEYLWE--EFSHVSVERVLSGMGIVRLYTFLAKDIPAPNRP----------LPIPK 282

Query: 233 EEKSVDPGAAIGTAALEKRDRLSEQTLQLFIEAYGAEAGNLALKLLPYGGLYIAGGIAPK 292
            E   D  + I   AL+++D +  + L++F E    EA N+ LK+L  GG +I GGI  +
Sbjct: 283 AEPPADFPSQISQKALDEKDPVCMKALEMFAEILAQEASNMVLKVLARGGCFIGGGIPIR 342

Query: 293 ILPLIQNSGFLLNFTQKGRMRPLLEEIPVYIILNPQVGLIGAALCAAR 340
           I P +++  F   F +KGR   LL ++PV+IIL+P+  L+G+A  A+R
Sbjct: 343 IRPFLESVAFRRRFVEKGRYSELLAKVPVWIILDPEAPLVGSAFYASR 390


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: 320
Number of extensions: 18
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: 400
Length adjustment: 30
Effective length of query: 311
Effective length of database: 370
Effective search space:   115070
Effective search space used:   115070
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_081495339.1 LFE_RS04280 (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.3696649.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.7e-77  246.7   0.0    2.1e-77  246.5   0.0    1.1  1  NCBI__GCF_000284315.1:WP_081495339.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000284315.1:WP_081495339.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  246.5   0.0   2.1e-77   2.1e-77       1     315 []      57     385 ..      57     385 .. 0.94

  Alignments for each domain:
  == domain 1  score: 246.5 bits;  conditional E-value: 2.1e-77
                             TIGR00749   1 lvgdiGGtnarlalvevapgeieqv......ktyssedfpsleavvrvyleeakvel.kdpi..kgcfaiatP 64 
                                           lvgdiGGt++ lal   a +  +         +y s+ ++sle++++ yl+  ++ l +dp    ++f +a+P
  NCBI__GCF_000284315.1:WP_081495339.1  57 LVGDIGGTKTSLALFSLAERGSREHfvplcpAVYPSKRYDSLEPMIQEYLSWVRERLvGDPNivAATFGVAGP 129
                                           89*************8888777665567889********************999875267644699******* PP

                             TIGR00749  65 iigdfvrltnldWalsieelkqelala..klelindfaavayailalkeedliqlggakveesaaiailGaGt 135
                                           ++g ++r tnl W +    l++ ++++  +++l+nd+ a a+++ +     l+ ++  ++ +s+++ ++ +Gt
  NCBI__GCF_000284315.1:WP_081495339.1 130 VTGRVCRTTNLPWIVDAGSLEKLISVQegNVNLLNDLEALAWSVGGDPLIPLATIQEGEPGTSTTMVLVAPGT 202
                                           ************************99834699**************9999*********************** PP

                             TIGR00749 136 GlGvatliqqsdgrykvlageGghvdfaPrseleillleylrkkygrvsaervlsGsGlvliyealskrkger 208
                                           GlG a l    d+++ +l++eGgh+d+aP +++++ lleyl +++++vs+ervlsG+G+v +y +l k  +  
  NCBI__GCF_000284315.1:WP_081495339.1 203 GLGEAVLCG-RDENFFALPSEGGHADWAPVNKEQARLLEYLWEEFSHVSVERVLSGMGIVRLYTFLAKDIPAP 274
                                           *****9998.899********************************************************9887 PP

                             TIGR00749 209 e....vsklskeelkekdiseaalegsdvlarralelflsilGalagnlalklgarGGvyvaGGivPrfiell 277
                                           +    + k       + +is++al+++d+++ +ale+f  il ++a+n+ lk++arGG ++ GGi  r+ ++l
  NCBI__GCF_000284315.1:WP_081495339.1 275 NrplpIPKAEPPADFPSQISQKALDEKDPVCMKALEMFAEILAQEASNMVLKVLARGGCFIGGGIPIRIRPFL 347
                                           766777777777888999******************************************************* PP

                             TIGR00749 278 kkssfraafedkGrlkellasiPvqvvlkkkvGllGag 315
                                           ++ +fr +f +kGr+ ella++Pv ++l+ ++ l+G++
  NCBI__GCF_000284315.1:WP_081495339.1 348 ESVAFRRRFVEKGRYSELLAKVPVWIILDPEAPLVGSA 385
                                           ***********************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (315 nodes)
Target sequences:                          1  (400 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: 19.86
//
[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