Alignments for a candidate for deoK in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoK in Pseudomonas simiae WCS417

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate GFF3591 PS417_18385 ribokinase

Query= reanno::pseudo3_N2E3:AO353_20835
         (305 letters)



>FitnessBrowser__WCS417:GFF3591
          Length = 305

 Score =  477 bits (1228), Expect = e-139
 Identities = 245/305 (80%), Positives = 274/305 (89%)

Query: 1   MPAKVVVVGSLNMDLVTRAQRLPHAGETLHGESFATVSGGKGANQAVASARLGAQVSMIG 60
           MPAKVVVVGSLNMDLVTRA RLP AGETL G++F+TV GGKGANQAVASARLGA VSMIG
Sbjct: 1   MPAKVVVVGSLNMDLVTRASRLPRAGETLIGQTFSTVPGGKGANQAVASARLGADVSMIG 60

Query: 61  CVGDDAYGEQLRAALLAEQIDCQALTSVEGSSGVALIVVDDNSQNAIVIVAGANGQLTPG 120
           CVG DAYG QLR ALL E IDCQA+++V+GSSGVALIVVDD+SQNAIVIVAG+NG+LTP 
Sbjct: 61  CVGSDAYGSQLREALLVEGIDCQAVSTVDGSSGVALIVVDDSSQNAIVIVAGSNGELTPA 120

Query: 121 MVAGFDAVLAAADVIICQLEVPMHTVGYVLKRGRELGKTVILNPAPATSPLPADWYSSID 180
            +  FDAVL AADVI+CQLEVPM+TVGY LKRGRELGKTVILNPAPA+ PLPA+WY+SID
Sbjct: 121 SLQAFDAVLQAADVIVCQLEVPMNTVGYALKRGRELGKTVILNPAPASGPLPAEWYASID 180

Query: 181 YLIPNESEASALSGLPVDSLESAELAASRLIAAGAGKVIITLGPQGSLFANGQSCEHFPA 240
           YLIPNESEASALSG+ VDS+++A++AA++LI AGAGKVI+TLG QG+LF +GQ  EH  A
Sbjct: 181 YLIPNESEASALSGVTVDSIDAAKVAATQLIQAGAGKVIVTLGAQGALFTDGQRFEHLQA 240

Query: 241 PKVKSVDTTAAGDTFVGGFAAALAAGKSEVEAIRFGQVAAALSVTRAGAQPSIPSLSDVQ 300
           PKVK+VDTTAAGDTFVGGFAAALA GKSE EAIRFGQVAAALSVTRAGAQPSIP+L DVQ
Sbjct: 241 PKVKAVDTTAAGDTFVGGFAAALANGKSEAEAIRFGQVAAALSVTRAGAQPSIPTLHDVQ 300

Query: 301 AFKAS 305
            F  S
Sbjct: 301 GFVPS 305


Lambda     K      H
   0.315    0.130    0.363 

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: 396
Number of extensions: 6
Number of successful extensions: 2
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: 305
Length of database: 305
Length adjustment: 27
Effective length of query: 278
Effective length of database: 278
Effective search space:    77284
Effective search space used:    77284
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: 48 (23.1 bits)

Align candidate GFF3591 PS417_18385 (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.3296.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   4.7e-116  373.3   6.4   5.2e-116  373.1   6.4    1.0  1  lcl|FitnessBrowser__WCS417:GFF3591  PS417_18385 ribokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF3591  PS417_18385 ribokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.1   6.4  5.2e-116  5.2e-116       1     297 [.       5     300 ..       5     301 .. 0.99

  Alignments for each domain:
  == domain 1  score: 373.1 bits;  conditional E-value: 5.2e-116
                           TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgeellenlkkeg 75 
                                         +vvvGS+n+Dlv+r++rlp++Get+ +++f++++GGKGANQAva arlga+vsmig+vG+D++g++l+e+l  eg
  lcl|FitnessBrowser__WCS417:GFF3591   5 VVVVGSLNMDLVTRASRLPRAGETLIGQTFSTVPGGKGANQAVASARLGADVSMIGCVGSDAYGSQLREALLVEG 79 
                                         79************************************************************************* PP

                           TIGR02152  76 idteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekikesdlvllQlEipletveealkia 150
                                         id++ v++v + s+GvAli+vd++++N+Iv+vaG+n eltp+ ++a  + ++++d++++QlE+p++tv +alk  
  lcl|FitnessBrowser__WCS417:GFF3591  80 IDCQAVSTV-DGSSGVALIVVDDSSQNAIVIVAGSNGELTPASLQAFDAVLQAADVIVCQLEVPMNTVGYALKRG 153
                                         *******99.5677************************************************************* PP

                           TIGR02152 151 kkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedledaekaaekllekgvkaviitlGskGal 225
                                         ++ g++v+lnPAPa+  l++e+++ +d+++pNe+Ea++L+g++v+++++a+ aa++l + g+ +vi+tlG++Gal
  lcl|FitnessBrowser__WCS417:GFF3591 154 RELGKTVILNPAPASGPLPAEWYASIDYLIPNESEASALSGVTVDSIDAAKVAATQLIQAGAGKVIVTLGAQGAL 228
                                         *************************************************************************** PP

                           TIGR02152 226 lvskdekklipalkvkavDttaAGDtFigalavaLaegksledavrfanaaaalsVtrkGaqssiPtkeeve 297
                                         +++ ++ ++++a kvkavDttaAGDtF+g++a+aLa+gks ++a+rf++ aaalsVtr+Gaq+siPt+++v+
  lcl|FitnessBrowser__WCS417:GFF3591 229 FTDGQRFEHLQAPKVKAVDTTAAGDTFVGGFAAALANGKSEAEAIRFGQVAAALSVTRAGAQPSIPTLHDVQ 300
                                         *********************************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (305 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: 00:00:00.02
# Mc/sec: 3.46
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
Protein sequences (fasta format)
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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