Alignments for a candidate for rbsK in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsK in Pseudomonas fluorescens FW300-N2E2

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate Pf6N2E2_165 Ribokinase (EC 2.7.1.15)

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



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_165
          Length = 304

 Score =  554 bits (1427), Expect = e-162
 Identities = 287/304 (94%), Positives = 294/304 (96%)

Query: 1   MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGESFATIPGGKGANQAVAAARLGAQVSMVG 60
           MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGESF+TIPGGKGANQAVAAARLGA+VSMVG
Sbjct: 1   MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGESFSTIPGGKGANQAVAAARLGAEVSMVG 60

Query: 61  CVGDDAYGEQLRGALLAEGIDCQAVRVEQGSSGVALIVVDDNSQNAIVIVAGANGALTAE 120
           CVG+DAYGEQLRG LLAEGIDCQAV V +G+SGVALIVVDDNSQNAIVIVAGANGALTAE
Sbjct: 61  CVGNDAYGEQLRGGLLAEGIDCQAVSVVEGASGVALIVVDDNSQNAIVIVAGANGALTAE 120

Query: 121 VLDGVDDVLQSADVIICQLEVPDATVGHALKRGRALGKIVILNPAPASHALPADWYACID 180
           VLD VD+VLQSADVIICQLEVPDATVGHALKR R LGKIVILNPAPASH LPADWYACID
Sbjct: 121 VLDSVDEVLQSADVIICQLEVPDATVGHALKRARELGKIVILNPAPASHTLPADWYACID 180

Query: 181 YLIPNESEAAVLSGLAVDSLETAEAAAAHLIAAGAGKVIVTLGAQGLMFANGASFEHFPA 240
           YL+PNESEAAVLSGLAVDSLETAEAAAAHLIAAGAGKVIVTLGAQGLMFANG SFEHFPA
Sbjct: 181 YLVPNESEAAVLSGLAVDSLETAEAAAAHLIAAGAGKVIVTLGAQGLMFANGVSFEHFPA 240

Query: 241 PRVKAVDTTAAGDTFVGGFAAALACGKSEVDAIRFGQVAAALSVTRAGAQPSIPTLLEVQ 300
           PRVKAVDTTAAGDTFVGGFAAALA GKSEVDAIRFGQ AAALSVTRAGAQPSIPTLLEVQ
Sbjct: 241 PRVKAVDTTAAGDTFVGGFAAALASGKSEVDAIRFGQAAAALSVTRAGAQPSIPTLLEVQ 300

Query: 301 AFKS 304
           AFKS
Sbjct: 301 AFKS 304


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: 484
Number of extensions: 12
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: 304
Length of database: 304
Length adjustment: 27
Effective length of query: 277
Effective length of database: 277
Effective search space:    76729
Effective search space used:    76729
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 Pf6N2E2_165 (Ribokinase (EC 2.7.1.15))
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.10487.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
     3e-116  373.9   6.1   3.3e-116  373.7   6.1    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_165  Ribokinase (EC 2.7.1.15)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_165  Ribokinase (EC 2.7.1.15)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.7   6.1  3.3e-116  3.3e-116       1     297 [.       5     300 ..       5     301 .. 0.99

  Alignments for each domain:
  == domain 1  score: 373.7 bits;  conditional E-value: 3.3e-116
                                     TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefge 65 
                                                   +vv+GS+n+Dlv+r++rlp+ Get+ +e+f++++GGKGANQAvaaarlgaevsm+g+vG+D++ge
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_165   5 VVVIGSLNMDLVTRAPRLPRGGETLIGESFSTIPGGKGANQAVAAARLGAEVSMVGCVGNDAYGE 69 
                                                   79*************************************************************** PP

                                     TIGR02152  66 ellenlkkegidteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekikesd 130
                                                   +l+  l +egid++ v+ v+  ++GvAli+vd++++N+Iv+vaGan  lt+e++++  e ++++d
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_165  70 QLRGGLLAEGIDCQAVSVVEG-ASGVALIVVDDNSQNAIVIVAGANGALTAEVLDSVDEVLQSAD 133
                                                   *****************9966.56***************************************** PP

                                     TIGR02152 131 lvllQlEipletveealkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgieve 195
                                                   ++++QlE+p +tv +alk a++ g+ v+lnPAPa+++l++++++ +d++vpNe+Ea++L+g +v+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_165 134 VIICQLEVPDATVGHALKRARELGKIVILNPAPASHTLPADWYACIDYLVPNESEAAVLSGLAVD 198
                                                   ***************************************************************** PP

                                     TIGR02152 196 dledaekaaekllekgvkaviitlGskGallvskdekklipalkvkavDttaAGDtFigalavaL 260
                                                   +le+ae+aa++l + g+ +vi+tlG++G ++++  + +++pa +vkavDttaAGDtF+g++a+aL
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_165 199 SLETAEAAAAHLIAAGAGKVIVTLGAQGLMFANGVSFEHFPAPRVKAVDTTAAGDTFVGGFAAAL 263
                                                   ***************************************************************** PP

                                     TIGR02152 261 aegksledavrfanaaaalsVtrkGaqssiPtkeeve 297
                                                   a+gks  da+rf++aaaalsVtr+Gaq+siPt+ ev+
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_165 264 ASGKSEVDAIRFGQAAAALSVTRAGAQPSIPTLLEVQ 300
                                                   ***********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (304 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: 00:00:00.00
# Mc/sec: 11.35
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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