Alignments for a candidate for rbsK in Lactobacillus pobuzihii E100301

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsK in Lactobacillus pobuzihii E100301

Align Ribokinase; RK; EC 2.7.1.15 (uncharacterized)
to candidate WP_017868726.1 LACPOB_RS12085 ribokinase

Query= curated2:Q9CF42
         (300 letters)



>NCBI__GCF_000349725.1:WP_017868726.1
          Length = 271

 Score =  158 bits (400), Expect = 1e-43
 Identities = 109/269 (40%), Positives = 156/269 (57%), Gaps = 16/269 (5%)

Query: 38  GGKGANQAVAFARLSPNEVSMIGAVGKDAFGESILQNFKENAVLFENVGTVPQTTGIAQI 97
           GGKG+NQA+A +RL  + V++I AVG D FG+  L+N+K N +   NV    + +GIA I
Sbjct: 2   GGKGSNQAIAASRLG-STVNLITAVGNDDFGKQQLENYKRNNIDTHNVIIGNEISGIAPI 60

Query: 98  TLYDD-DNRIIIIPGANNEVLPSYLADLWEKI-KESQLVILQNEIPHETNLAIAKFCKEN 155
            + ++ +N III+ GANNE L S   D +EKI   S+L++LQ EIP ETN  + K   + 
Sbjct: 61  FVKENGENSIIIVKGANNE-LTSQKVDQYEKIIAGSKLIVLQQEIPLETNNEVIKIANKY 119

Query: 156 AIKVLYNPAPAR-KTDLEMIDFVDYITPNEHECKELFPNL----------ALEEILKKYS 204
            + VL NPAPA  +  L+ I  V +  PNE E   +  NL          A ++I+K   
Sbjct: 120 NVPVLLNPAPASDEVSLDNISKVQFYAPNETELARI-TNLPVNTIDEIKSAAQQIVKAGV 178

Query: 205 NRLIVTLGSEGVIFHDGETLQKIPAIKAKVVDTTGAGDTFNGAFAFGLTENLSISDSIRL 264
           + +IVTLG +G ++   E  + IP+ K  VVDTTGAGD F G+FA   T    I  S+  
Sbjct: 179 DNVIVTLGEKGALWVTQENHKLIPSKKVDVVDTTGAGDAFIGSFAHYYTSGQDIETSLSA 238

Query: 265 AVVASHLSIQKFGAQGGMPKLSEVKAKLK 293
           A + + L+I+K G Q      +EV+ +LK
Sbjct: 239 ANIYAALTIKKRGTQKSYLSYNEVEEELK 267


Lambda     K      H
   0.316    0.135    0.376 

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: 228
Number of extensions: 14
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: 300
Length of database: 271
Length adjustment: 26
Effective length of query: 274
Effective length of database: 245
Effective search space:    67130
Effective search space used:    67130
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 (21.6 bits)
S2: 47 (22.7 bits)

Align candidate WP_017868726.1 LACPOB_RS12085 (ribokinase)
to HMM TIGR02152 (rbsK: ribokinase (EC 2.7.1.15))

# 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/TIGR02152.hmm
# target sequence database:        /tmp/gapView.3439160.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02152  [M=298]
Accession:   TIGR02152
Description: D_ribokin_bact: ribokinase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
      7e-98  313.6   7.3    7.9e-98  313.4   7.3    1.0  1  NCBI__GCF_000349725.1:WP_017868726.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000349725.1:WP_017868726.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  313.4   7.3   7.9e-98   7.9e-98      34     298 .]       1     264 [.       1     264 [. 0.99

  Alignments for each domain:
  == domain 1  score: 313.4 bits;  conditional E-value: 7.9e-98
                             TIGR02152  34 aGGKGANQAvaaarlgaevsmigkvGkDefgeellenlkkegidteyvkkvkktstGvAlilvdeegeNsIvv 106
                                           +GGKG+NQA+aa+rlg++v++i++vG+D+fg++ len+k+++idt++v  + ++ +G+A i+v+e+geNsI++
  NCBI__GCF_000349725.1:WP_017868726.1   1 YGGKGSNQAIAASRLGSTVNLITAVGNDDFGKQQLENYKRNNIDTHNVI-IGNEISGIAPIFVKENGENSIII 72 
                                           5***********************************************9.567778***************** PP

                             TIGR02152 107 vaGaneeltpedvkaaeekikesdlvllQlEipletveealkiakkagvkvllnPAPaekkldeellslvdii 179
                                           v+Gan+elt+++v+++e+ i+ s+l++lQ+Eiplet++e++kia+k +v vllnPAPa+++++ + +s+v++ 
  NCBI__GCF_000349725.1:WP_017868726.1  73 VKGANNELTSQKVDQYEKIIAGSKLIVLQQEIPLETNNEVIKIANKYNVPVLLNPAPASDEVSLDNISKVQFY 145
                                           ************************************************************************* PP

                             TIGR02152 180 vpNetEaeiLtgievedledaekaaekllekgvkaviitlGskGallvskdekklipalkvkavDttaAGDtF 252
                                            pNetE++ +t+  v++++++++aa+++ + gv++vi+tlG+kGal+v+++++klip+ kv++vDtt+AGD+F
  NCBI__GCF_000349725.1:WP_017868726.1 146 APNETELARITNLPVNTIDEIKSAAQQIVKAGVDNVIVTLGEKGALWVTQENHKLIPSKKVDVVDTTGAGDAF 218
                                           ************************************************************************* PP

                             TIGR02152 253 igalavaLaegksledavrfanaaaalsVtrkGaqssiPtkeevee 298
                                           ig++a++ ++g+++e++++ an +aal++++ G+q+s+ + +evee
  NCBI__GCF_000349725.1:WP_017868726.1 219 IGSFAHYYTSGQDIETSLSAANIYAALTIKKRGTQKSYLSYNEVEE 264
                                           *******************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (271 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 12.66
//
[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