Alignments for a candidate for rbsK in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsK in Burkholderia phytofirmans PsJN

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate BPHYT_RS20695 BPHYT_RS20695 ribokinase

Query= reanno::pseudo1_N1B4:Pf1N1B4_6031
         (305 letters)



>FitnessBrowser__BFirm:BPHYT_RS20695
          Length = 310

 Score =  315 bits (808), Expect = 7e-91
 Identities = 167/300 (55%), Positives = 213/300 (71%), Gaps = 2/300 (0%)

Query: 4   KVVVIGSLNMDLVTRAPRLPRGGETLIGKSFATVSGGKGANQAVAAARLGAQVSMVGCVG 63
           +V+V+GS+N DLV RAP LPR GET+ G  F+ V+GGKG NQAVAAAR+GAQV+MVGCVG
Sbjct: 9   RVLVVGSINTDLVARAPHLPRPGETIGGHEFSQVAGGKGGNQAVAAARIGAQVAMVGCVG 68

Query: 64  NDAYGEALRGALLAEQIDCQAVSTVEDS-SGVALIVVDDNSQNAIVIVAGANGALTPEVI 122
            DA G      L AE IDC  +       +GVA++ V D+ QN IV+VAG+NG LTPE +
Sbjct: 69  KDANGAQRVKDLEAEGIDCSGIEVHPGQPTGVAMVTVSDDGQNTIVVVAGSNGELTPESV 128

Query: 123 DRFDAVLQAADVIICQLEVPDATVGHALKRGRELGKTVILNPAPASRPLPVDWYAAIDYL 182
            R +A ++A DV++CQLE P  +V   L   R LGK  +LNPAPA+ PLP +W   +DYL
Sbjct: 129 ARHEAAIKACDVVVCQLETPWDSVHATLALARRLGKITVLNPAPATGPLPAEWLPLVDYL 188

Query: 183 IPNESEASVLSGLPVDSLSTAETAATRLIAMGAGKVIITLGSQGS-LFADGQRFEHFPAA 241
           +PNE EA++L+GLPV+S S A  AAT L   GA  VI+TLG+QG+ L  +G    HFPA 
Sbjct: 189 VPNEVEAAILAGLPVESQSGARRAATELQQGGARNVIVTLGAQGAYLLVEGGEGMHFPAP 248

Query: 242 KVKAVDTTAAGDTFVGGFAAALAAGKGEADAIRFGQVAAALSVTRAGAQPSIPTLSDVQA 301
           +V+AVDTTAAGDTF+G FAA LA+ +    AI   Q AA++SVTRAGAQPSIPT ++V +
Sbjct: 249 QVQAVDTTAAGDTFIGVFAAQLASRQPLESAISLAQRAASISVTRAGAQPSIPTRAEVDS 308


Lambda     K      H
   0.316    0.132    0.369 

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: 306
Number of extensions: 10
Number of successful extensions: 3
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: 310
Length adjustment: 27
Effective length of query: 278
Effective length of database: 283
Effective search space:    78674
Effective search space used:    78674
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 BPHYT_RS20695 BPHYT_RS20695 (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.31453.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   4.1e-116  373.5   2.3   4.6e-116  373.3   2.3    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS20695  BPHYT_RS20695 ribokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS20695  BPHYT_RS20695 ribokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.3   2.3  4.6e-116  4.6e-116       1     297 [.      10     307 ..      10     308 .. 0.99

  Alignments for each domain:
  == domain 1  score: 373.3 bits;  conditional E-value: 4.6e-116
                                TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgeellen 70 
                                              ++vvGSin+Dlv+r+++lp+pGet+ ++ef+++aGGKG NQAvaaar+ga+v+m+g+vGkD+ g++ +++
  lcl|FitnessBrowser__BFirm:BPHYT_RS20695  10 VLVVGSINTDLVARAPHLPRPGETIGGHEFSQVAGGKGGNQAVAAARIGAQVAMVGCVGKDANGAQRVKD 79 
                                              79******************************************************************** PP

                                TIGR02152  71 lkkegidteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekikesdlvllQlEipl 140
                                              l++egid++ ++ +  ++tGvA+++v+++g+N+IvvvaG+n eltpe v+++e++ik++d+v++QlE+p 
  lcl|FitnessBrowser__BFirm:BPHYT_RS20695  80 LEAEGIDCSGIEVHPGQPTGVAMVTVSDDGQNTIVVVAGSNGELTPESVARHEAAIKACDVVVCQLETPW 149
                                              ********************************************************************** PP

                                TIGR02152 141 etveealkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedledaekaaekllek 210
                                              ++v++ l +a++ g+ ++lnPAPa+  l++e+l lvd++vpNe Ea+iL g  ve+++ a++aa++l++ 
  lcl|FitnessBrowser__BFirm:BPHYT_RS20695 150 DSVHATLALARRLGKITVLNPAPATGPLPAEWLPLVDYLVPNEVEAAILAGLPVESQSGARRAATELQQG 219
                                              ********************************************************************** PP

                                TIGR02152 211 gvkaviitlGskGallvskd.ekklipalkvkavDttaAGDtFigalavaLaegksledavrfanaaaal 279
                                              g+++vi+tlG++Ga+l+ ++ e  ++pa +v+avDttaAGDtFig +a++La+ + le+a++ a++aa++
  lcl|FitnessBrowser__BFirm:BPHYT_RS20695 220 GARNVIVTLGAQGAYLLVEGgEGMHFPAPQVQAVDTTAAGDTFIGVFAAQLASRQPLESAISLAQRAASI 289
                                              **************998777699*********************************************** PP

                                TIGR02152 280 sVtrkGaqssiPtkeeve 297
                                              sVtr+Gaq+siPt++ev+
  lcl|FitnessBrowser__BFirm:BPHYT_RS20695 290 SVTRAGAQPSIPTRAEVD 307
                                              ****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (310 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.70
//
[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