Alignments for a candidate for deoK in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoK in Burkholderia phytofirmans PsJN

Align deoxyribose kinase (EC 2.7.1.15) (characterized)
to candidate BPHYT_RS25805 BPHYT_RS25805 ribokinase

Query= reanno::BFirm:BPHYT_RS25805
         (328 letters)



>FitnessBrowser__BFirm:BPHYT_RS25805
          Length = 328

 Score =  640 bits (1652), Expect = 0.0
 Identities = 328/328 (100%), Positives = 328/328 (100%)

Query: 1   MNTPAQLNGKGRVVILGIYVTDLTFRAGRMPQIGETIAGTAFAMGPGGKGSNQAVAAARV 60
           MNTPAQLNGKGRVVILGIYVTDLTFRAGRMPQIGETIAGTAFAMGPGGKGSNQAVAAARV
Sbjct: 1   MNTPAQLNGKGRVVILGIYVTDLTFRAGRMPQIGETIAGTAFAMGPGGKGSNQAVAAARV 60

Query: 61  GADVVFCTRIGNDAFGSIARATWAAEGITARASVIDGVSTGAAHIFVDDNTGMNAIIVAS 120
           GADVVFCTRIGNDAFGSIARATWAAEGITARASVIDGVSTGAAHIFVDDNTGMNAIIVAS
Sbjct: 61  GADVVFCTRIGNDAFGSIARATWAAEGITARASVIDGVSTGAAHIFVDDNTGMNAIIVAS 120

Query: 121 GAAGTMEAADVDAIEADIAAARVFVTQLEQPLAAARRGLEVARKHGVITVFNPAPAMPLD 180
           GAAGTMEAADVDAIEADIAAARVFVTQLEQPLAAARRGLEVARKHGVITVFNPAPAMPLD
Sbjct: 121 GAAGTMEAADVDAIEADIAAARVFVTQLEQPLAAARRGLEVARKHGVITVFNPAPAMPLD 180

Query: 181 DAIFPLCDYITPNETEATALTGVPIANADDARRAADVLLAKGVGTAIITLGEGGALLHSA 240
           DAIFPLCDYITPNETEATALTGVPIANADDARRAADVLLAKGVGTAIITLGEGGALLHSA
Sbjct: 181 DAIFPLCDYITPNETEATALTGVPIANADDARRAADVLLAKGVGTAIITLGEGGALLHSA 240

Query: 241 NQSLLVPAYHCGRVVETAGAGDGFTGGFAAALARGDDAITALRFGCALAGISVTRPGTAP 300
           NQSLLVPAYHCGRVVETAGAGDGFTGGFAAALARGDDAITALRFGCALAGISVTRPGTAP
Sbjct: 241 NQSLLVPAYHCGRVVETAGAGDGFTGGFAAALARGDDAITALRFGCALAGISVTRPGTAP 300

Query: 301 SMPTLDEVNQVLNQPSQPNQAAGVSQPS 328
           SMPTLDEVNQVLNQPSQPNQAAGVSQPS
Sbjct: 301 SMPTLDEVNQVLNQPSQPNQAAGVSQPS 328


Lambda     K      H
   0.318    0.133    0.384 

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: 520
Number of extensions: 17
Number of successful extensions: 1
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: 328
Length of database: 328
Length adjustment: 28
Effective length of query: 300
Effective length of database: 300
Effective search space:    90000
Effective search space used:    90000
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: 49 (23.5 bits)

Align candidate BPHYT_RS25805 BPHYT_RS25805 (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.19381.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
    4.3e-94  301.1   4.9    4.9e-94  301.0   4.9    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS25805  BPHYT_RS25805 ribokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS25805  BPHYT_RS25805 ribokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  301.0   4.9   4.9e-94   4.9e-94       1     298 []      13     310 ..      13     310 .. 0.97

  Alignments for each domain:
  == domain 1  score: 301.0 bits;  conditional E-value: 4.9e-94
                                TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgeellen 70 
                                              +v++G + +Dl++r+ r+p+ Get++++ f +++GGKG+NQAvaaar+ga+v + +++G+D+fg+ ++ +
  lcl|FitnessBrowser__BFirm:BPHYT_RS25805  13 VVILGIYVTDLTFRAGRMPQIGETIAGTAFAMGPGGKGSNQAVAAARVGADVVFCTRIGNDAFGSIARAT 82 
                                              799******************************************************************* PP

                                TIGR02152  71 lkkegidteyvkkvkktstGvAlilvde.egeNsIvvvaGaneeltpedvkaaeekikesdlvllQlEip 139
                                              +++egi t   + ++ +stG A+i+vd+ +g N+I+v++Ga  +++++dv+a e++i+++++ + QlE p
  lcl|FitnessBrowser__BFirm:BPHYT_RS25805  83 WAAEGI-TARASVIDGVSTGAAHIFVDDnTGMNAIIVASGAAGTMEAADVDAIEADIAAARVFVTQLEQP 151
                                              ******.7778999************872699************************************** PP

                                TIGR02152 140 letveealkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedledaekaaeklle 209
                                              l+++++ l++a+k+gv +++nPAPa + ld+ ++ l+d+i+pNetEa +Ltg+ +++++da++aa+ ll+
  lcl|FitnessBrowser__BFirm:BPHYT_RS25805 152 LAAARRGLEVARKHGVITVFNPAPAMP-LDDAIFPLCDYITPNETEATALTGVPIANADDARRAADVLLA 220
                                              *************************77.99**************************************** PP

                                TIGR02152 210 kgvkaviitlGskGallvskdekklipalkv.kavDttaAGDtFigalavaLaegksledavrfanaaaa 278
                                              kgv + iitlG+ Gall+s++++ l+pa++  ++v t++AGD F+g++a+aLa+g+++ +a+rf+ a+a 
  lcl|FitnessBrowser__BFirm:BPHYT_RS25805 221 KGVGTAIITLGEGGALLHSANQSLLVPAYHCgRVVETAGAGDGFTGGFAAALARGDDAITALRFGCALAG 290
                                              ****************************9874799*********************************** PP

                                TIGR02152 279 lsVtrkGaqssiPtkeevee 298
                                              +sVtr G+++s+Pt++ev++
  lcl|FitnessBrowser__BFirm:BPHYT_RS25805 291 ISVTRPGTAPSMPTLDEVNQ 310
                                              ******************85 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (328 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 11.06
//
[ok]

This GapMind analysis is from Sep 17 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