Alignments for a candidate for deoK in Chromobacterium vaccinii MWU205

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoK in Chromobacterium vaccinii MWU205

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate WP_046158456.1 VL52_RS18705 ribokinase

Query= reanno::pseudo5_N2C3_1:AO356_00950
         (304 letters)



>NCBI__GCF_000971335.1:WP_046158456.1
          Length = 296

 Score =  241 bits (614), Expect = 2e-68
 Identities = 144/300 (48%), Positives = 182/300 (60%), Gaps = 12/300 (4%)

Query: 4   KVVVIGSLNMDLVTRAPRLPRGGETLIGESFATIPGGKGANQAVAAARLGAQVSMVGCVG 63
           +V+V+GS+NMDLV  A R+P+ GETL+GE F+T PGGKGANQAVAAARLGAQV+++GCVG
Sbjct: 3   RVLVVGSINMDLVASAKRMPKLGETLLGEGFSTYPGGKGANQAVAAARLGAQVTLLGCVG 62

Query: 64  DDAYGEQLRGALLAEGIDCQAVRVEQGSSGVALIVVDDNSQNAIVIVAGANGALTAEVLD 123
           DDA+G  LR  L  EG+DC  V    G +G+A+I V     NAI++V GAN  LT   LD
Sbjct: 63  DDAFGRDLRAHLEREGVDCGRVETVDGPTGIAVITV-SGGDNAILVVPGANHKLTPVHLD 121

Query: 124 GVDDVLQSADVIICQLEVPDATVGHALKRGRALGKIVILNPAPASHALPADWYACIDYLI 183
             +     ADV++ QLE+P ATV  A +      K ++LNPAPA   LP +    +  L 
Sbjct: 122 AAEQAFIDADVVLTQLEIPLATVRRAAELAARHKKPLLLNPAPAV-PLPEELLQRVALLT 180

Query: 184 PNESEAAVLSGLAVDSLETAEAAAAHLIAAGAGKVIVTLGAQGLMFANG-ASFEHFPAPR 242
           PNE E   +       L   +A    L+A   GK+++T G  G  FA       H P   
Sbjct: 181 PNEHEFLTM-------LAQPDADWRSLLAERPGKLVMTHGKHGAYFALARGQLRHQPGFE 233

Query: 243 VKAVDTTAAGDTFVGGFAAALACGKSEVDAIRFGQVAAALSVTRAGAQPSIPTLLEVQAF 302
           VKAVD+T AGDTF G  AA L  G  E  A+R    A ALSVTR GAQ  +PTL E++AF
Sbjct: 234 VKAVDSTGAGDTFNGALAAFLPLGLEE--AVRRANAAGALSVTRPGAQGGMPTLAELEAF 291


Lambda     K      H
   0.318    0.133    0.377 

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: 258
Number of extensions: 10
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: 304
Length of database: 296
Length adjustment: 27
Effective length of query: 277
Effective length of database: 269
Effective search space:    74513
Effective search space used:    74513
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: 48 (23.1 bits)

Align candidate WP_046158456.1 VL52_RS18705 (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.1119861.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
    1.9e-96  308.9   0.0    2.2e-96  308.7   0.0    1.0  1  NCBI__GCF_000971335.1:WP_046158456.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000971335.1:WP_046158456.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.7   0.0   2.2e-96   2.2e-96       1     297 [.       4     289 ..       4     290 .. 0.95

  Alignments for each domain:
  == domain 1  score: 308.7 bits;  conditional E-value: 2.2e-96
                             TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgeellenlkk 73 
                                           ++vvGSin+Dlv+++kr+pk Get+ +e f++++GGKGANQAvaaarlga+v+++g+vG+D+fg++l+ +l++
  NCBI__GCF_000971335.1:WP_046158456.1   4 VLVVGSINMDLVASAKRMPKLGETLLGEGFSTYPGGKGANQAVAAARLGAQVTLLGCVGDDAFGRDLRAHLER 76 
                                           79*********************************************************************** PP

                             TIGR02152  74 egidteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekikesdlvllQlEipletveea 146
                                           eg+d+  v++v + +tG+A+i+v+  g+N+I+vv Gan++ltp +++aae+++ ++d+vl QlEipl+tv++a
  NCBI__GCF_000971335.1:WP_046158456.1  77 EGVDCGRVETV-DGPTGIAVITVSG-GDNAILVVPGANHKLTPVHLDAAEQAFIDADVVLTQLEIPLATVRRA 147
                                           *********88.7899*******99.*********************************************** PP

                             TIGR02152 147 lkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedledaekaaekllekgvkaviitl 219
                                           +++a ++++  llnPAPa + l+eell+ v +++pNe+E+ +++ +        ++  + ll++   ++++t 
  NCBI__GCF_000971335.1:WP_046158456.1 148 AELAARHKKPLLLNPAPAVP-LPEELLQRVALLTPNEHEFLTMLAQP-------DADWRSLLAERPGKLVMTH 212
                                           ******************87.99****************99888886.......44455666666888***** PP

                             TIGR02152 220 GskGallvskd.ekklipalkvkavDttaAGDtFigalavaLaegksledavrfanaaaalsVtrkGaqssiP 291
                                           G++Ga+++ +  + ++ p ++vkavD t+AGDtF+gala+ L  g  le+avr+anaa alsVtr Gaq ++P
  NCBI__GCF_000971335.1:WP_046158456.1 213 GKHGAYFALARgQLRHQPGFEVKAVDSTGAGDTFNGALAAFLPLG--LEEAVRRANAAGALSVTRPGAQGGMP 283
                                           ******98776699****************************998..99************************ PP

                             TIGR02152 292 tkeeve 297
                                           t++e+e
  NCBI__GCF_000971335.1:WP_046158456.1 284 TLAELE 289
                                           ***997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (296 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: 18.80
//
[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