Alignments for a candidate for gntK in Lactobacillus shenzhenensis LY-73

GapMind for catabolism of small carbon sources

Alignments for a candidate for gntK in Lactobacillus shenzhenensis LY-73

Align Gluconokinase; EC 2.7.1.12; Gluconate kinase (uncharacterized)
to candidate WP_022529344.1 L248_RS06505 gluconokinase

Query= curated2:P46834
         (513 letters)



>NCBI__GCF_000469325.1:WP_022529344.1
          Length = 521

 Score =  528 bits (1361), Expect = e-154
 Identities = 258/509 (50%), Positives = 349/509 (68%), Gaps = 3/509 (0%)

Query: 1   MTSYMLGIDIGTTSTKAVLFSEKGDVIQKESIGYALYTPDISTAEQNPDEIFQAVIQSTA 60
           MT+Y++G+D+GTTSTK VLF  +G V+   +  Y LY      AE++P+EIF A I    
Sbjct: 1   MTNYLIGVDLGTTSTKVVLFDTRGQVVASANTPYPLYQDTPDMAEEDPEEIFDATIAGLT 60

Query: 61  KIMQQHPDKQPSF--ISFSSAMHSVIAMDENDKPLTSCITWADNRSEGWAHKIKEEMNGH 118
            +M++   K      +SFS+AMHS+I M +++ PLT  ITWADNR+  +A ++K+   G 
Sbjct: 61  AVMRRAHLKPGELAGVSFSAAMHSLILMGQDNTPLTRVITWADNRAAQYATELKDSGLGM 120

Query: 119 NVYKRTGTPIHPMAPLSKITWIVNEHPEIAVKAKKYIGIKEYIFKKLFDQYVVDYSLASA 178
            ++K TG P HPM+PL K+ W+  EHP++  +    IGIK+YI  +LF +YV DYSLA+A
Sbjct: 121 QLFKNTGVPTHPMSPLVKLRWLNAEHPDLMRQTAHVIGIKDYILHRLFGRYVQDYSLANA 180

Query: 179 MGMMNLKTLAWDEEALAIAGITPDHLSKLVPTTAIFHHCNPELAAMMGIDPQTPFVIGAS 238
            G+ N+ T+ WD++ALA+A +T D L +LV T       NP  A ++GID   PF+IGAS
Sbjct: 181 TGLFNIHTMDWDDQALAVAQVTRDQLPELVDTDYQLTGLNPAYADVIGIDSSVPFIIGAS 240

Query: 239 DGVLSNLGVNAIKKGEIAVTIGTSGAIRPIIDKPQTDEKGRIFCYALTENHWVIGGPVNN 298
           DG LSNLGVNAI  G +AVTIGTSGA+R + DKP  D +GR+F Y L    WV+GGPVNN
Sbjct: 241 DGTLSNLGVNAIDPGVLAVTIGTSGAVRVVTDKPVVDPQGRLFTYYLAPGRWVVGGPVNN 300

Query: 299 GGIVLRWIRDEFASSEIETAKRLGIDPYDVLTKIAERVRPGADGLLFHPYLAGERAPLWN 358
           GGIV RW+RD+  + E  TA+++ +D Y++LT IA ++  GADGLLFHPYL GERAP+W+
Sbjct: 301 GGIVFRWVRDQLFAPEKLTAEQMDVDSYELLTTIASKIPAGADGLLFHPYLGGERAPIWD 360

Query: 359 PDVPGSFFGLTMSHKKEHMIRAALEGVIYNLYTVFLALTECMDGPVARIQATGGFARSDV 418
            +  GSFFGLT  H + HM+RA LEG++YNLY V L + E + G    IQATGGFARS +
Sbjct: 361 ANARGSFFGLTRQHTRAHMVRATLEGIVYNLYMVML-MIEGITGKPQAIQATGGFARSAL 419

Query: 419 WRQMMADIFESEVVVPESYESSCLGACILGLYATGKIDSFDVVSDMIGSTHRHAPKEESA 478
           WRQM+ADIFE +V +PES+ESS LGA ++ +   G ID    V DM+G T+ H P     
Sbjct: 420 WRQMLADIFEQDVNIPESFESSALGAVVIAMKRLGLIDDLSAVKDMVGVTNTHHPDPSVF 479

Query: 479 KEYRKLMPLFINLSRALENEYTQIANYQR 507
             YR+L+P++I L+R L  EYT IA++QR
Sbjct: 480 PIYRELLPIWIRLTRELSTEYTAIADFQR 508


Lambda     K      H
   0.318    0.134    0.401 

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: 719
Number of extensions: 25
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: 513
Length of database: 521
Length adjustment: 35
Effective length of query: 478
Effective length of database: 486
Effective search space:   232308
Effective search space used:   232308
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_022529344.1 L248_RS06505 (gluconokinase)
to HMM TIGR01314 (gntK: gluconate kinase (EC 2.7.1.12))

# 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/TIGR01314.hmm
# target sequence database:        /tmp/gapView.3413804.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01314  [M=505]
Accession:   TIGR01314
Description: gntK_FGGY: gluconate kinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.4e-220  719.0   0.0   1.6e-220  718.8   0.0    1.0  1  NCBI__GCF_000469325.1:WP_022529344.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000469325.1:WP_022529344.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  718.8   0.0  1.6e-220  1.6e-220       1     505 []       4     508 ..       4     508 .. 0.99

  Alignments for each domain:
  == domain 1  score: 718.8 bits;  conditional E-value: 1.6e-220
                             TIGR01314   1 yligvdigttstkavlfeengkvvakesigyplytddvdvaeenleeifeavlvtikevskeleee.keikfv 72 
                                           yligvd+gttstk vlf+  g+vva+ +  yply+d  d+aee++eeif+a +  +  v+++ + +  e+  v
  NCBI__GCF_000469325.1:WP_022529344.1   4 YLIGVDLGTTSTKVVLFDTRGQVVASANTPYPLYQDTPDMAEEDPEEIFDATIAGLTAVMRRAHLKpGELAGV 76 
                                           9**********************************************************9987766156**** PP

                             TIGR01314  73 sfsaqmhslialdendkpltrlitwadnraakyaekikeekngfeiykrtgtpihpmaplskiiwlkaerkdi 145
                                           sfsa+mhsli + +++ pltr+itwadnraa+ya+++k++  g++++k tg p hpm+pl k+ wl+ae++d+
  NCBI__GCF_000469325.1:WP_022529344.1  77 SFSAAMHSLILMGQDNTPLTRVITWADNRAAQYATELKDSGLGMQLFKNTGVPTHPMSPLVKLRWLNAEHPDL 149
                                           ************************************************************************* PP

                             TIGR01314 146 fqkaakyleikeyifkrlfdtyvidyslasatgllnlkeldwdkealelagikeeqlpklvetteilknlkee 218
                                           ++++a+ ++ik+yi++rlf+ yv dysla atgl+n++++dwd++al +a ++++qlp+lv+t + l +l++ 
  NCBI__GCF_000469325.1:WP_022529344.1 150 MRQTAHVIGIKDYILHRLFGRYVQDYSLANATGLFNIHTMDWDDQALAVAQVTRDQLPELVDTDYQLTGLNPA 222
                                           ************************************************************************* PP

                             TIGR01314 219 yakkmgidketkfvigasdgvlsnlgvnaikkgevavtigtsgairtvidkpktdekgrifcyalteehyvig 291
                                           ya  +gid++ +f+igasdg+lsnlgvnai++g++avtigtsga+r+v+dkp  d +gr+f+y l    +v+g
  NCBI__GCF_000469325.1:WP_022529344.1 223 YADVIGIDSSVPFIIGASDGTLSNLGVNAIDPGVLAVTIGTSGAVRVVTDKPVVDPQGRLFTYYLAPGRWVVG 295
                                           ************************************************************************* PP

                             TIGR01314 292 gpvnnggvvlrwlrdellaseietakrlgvdpydvltkiakrvkpgadgllfhpylageraplwnanargsff 364
                                           gpvnngg+v+rw+rd+l+a e  ta+++ vd y+ lt ia ++  gadgllfhpyl+gerap+w+anargsff
  NCBI__GCF_000469325.1:WP_022529344.1 296 GPVNNGGIVFRWVRDQLFAPEKLTAEQMDVDSYELLTTIASKIPAGADGLLFHPYLGGERAPIWDANARGSFF 368
                                           ************************************************************************* PP

                             TIGR01314 365 gltlshkkehmiraalegviynlytvalalvevvdetlkmikatggfaksevwrqllsdifesevvvpesyes 437
                                           glt  h + hm+ra+leg++ynly+v+l ++e + ++++ i+atggfa+s +wrq+l+dife++v++pes+es
  NCBI__GCF_000469325.1:WP_022529344.1 369 GLTRQHTRAHMVRATLEGIVYNLYMVML-MIEGITGKPQAIQATGGFARSALWRQMLADIFEQDVNIPESFES 440
                                           **************************99.57888888************************************ PP

                             TIGR01314 438 sclgaiilglkavgkiedlsavssmvgaterytpieenvkvyreivpifinlsrsleeeyeqiadfqr 505
                                           s lga+++++k +g i+dlsav++mvg t++++p +  + +yre+ pi+i+l+r l  ey+ iadfqr
  NCBI__GCF_000469325.1:WP_022529344.1 441 SALGAVVIAMKRLGLIDDLSAVKDMVGVTNTHHPDPSVFPIYRELLPIWIRLTRELSTEYTAIADFQR 508
                                           *******************************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (505 nodes)
Target sequences:                          1  (521 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: 35.02
//
[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 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