Alignments for a candidate for rbsK in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsK in Pseudomonas fluorescens GW456-L13

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate PfGW456L13_3908 Ribokinase (EC 2.7.1.15)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908
          Length = 305

 Score =  525 bits (1351), Expect = e-154
 Identities = 271/305 (88%), Positives = 287/305 (94%)

Query: 1   MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGKSFATVSGGKGANQAVAAARLGAQVSMVG 60
           M AKVVVIGSLNMDLVTRAPRLP+GGETLIG+SF TVSGGKGANQAVAAARLGAQVSM+G
Sbjct: 1   MSAKVVVIGSLNMDLVTRAPRLPKGGETLIGQSFTTVSGGKGANQAVAAARLGAQVSMIG 60

Query: 61  CVGNDAYGEALRGALLAEQIDCQAVSTVEDSSGVALIVVDDNSQNAIVIVAGANGALTPE 120
           CVGNDAYGEALRGALLAEQIDC+AVSTV+ SSGVALIVVDD+SQN+IVIV GANGALT E
Sbjct: 61  CVGNDAYGEALRGALLAEQIDCRAVSTVDGSSGVALIVVDDSSQNSIVIVPGANGALTAE 120

Query: 121 VIDRFDAVLQAADVIICQLEVPDATVGHALKRGRELGKTVILNPAPASRPLPVDWYAAID 180
            IDRFD+V++AADV+ICQLEVPDA+VGHALKRGRELGKTVILNPAPASRPLP DWYA+ID
Sbjct: 121 TIDRFDSVIRAADVLICQLEVPDASVGHALKRGRELGKTVILNPAPASRPLPSDWYASID 180

Query: 181 YLIPNESEASVLSGLPVDSLSTAETAATRLIAMGAGKVIITLGSQGSLFADGQRFEHFPA 240
           YLIPNESEAS LSGL VDSL TA+ AATRLIA+GAGKVIITLG+QGSLFADGQRFEHFPA
Sbjct: 181 YLIPNESEASALSGLSVDSLDTAQAAATRLIALGAGKVIITLGAQGSLFADGQRFEHFPA 240

Query: 241 AKVKAVDTTAAGDTFVGGFAAALAAGKGEADAIRFGQVAAALSVTRAGAQPSIPTLSDVQ 300
             VKAVDTTAAGDTFVGGFAAALAAG  EA AIRFGQVAAALSVTRAGAQPSIP LSDVQ
Sbjct: 241 PVVKAVDTTAAGDTFVGGFAAALAAGNDEAQAIRFGQVAAALSVTRAGAQPSIPALSDVQ 300

Query: 301 AFKAP 305
           AFK P
Sbjct: 301 AFKTP 305


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: 401
Number of extensions: 7
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 PfGW456L13_3908 (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.30922.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
     4e-115  370.2   2.4   4.4e-115  370.0   2.4    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908  Ribokinase (EC 2.7.1.15)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908  Ribokinase (EC 2.7.1.15)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  370.0   2.4  4.4e-115  4.4e-115       1     297 [.       5     300 ..       5     301 .. 0.99

  Alignments for each domain:
  == domain 1  score: 370.0 bits;  conditional E-value: 4.4e-115
                                               TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmi 55 
                                                             +vv+GS+n+Dlv+r++rlpk Get+ +++f++++GGKGANQAvaaarlga+vsmi
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908   5 VVVIGSLNMDLVTRAPRLPKGGETLIGQSFTTVSGGKGANQAVAAARLGAQVSMI 59 
                                                             79***************************************************** PP

                                               TIGR02152  56 gkvGkDefgeellenlkkegidteyvkkvkktstGvAlilvdeegeNsIvvvaGa 110
                                                             g+vG+D++ge+l+ +l +e+id+  v++v + s+GvAli+vd++++NsIv+v Ga
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908  60 GCVGNDAYGEALRGALLAEQIDCRAVSTV-DGSSGVALIVVDDSSQNSIVIVPGA 113
                                                             ***************************99.5677********************* PP

                                               TIGR02152 111 neeltpedvkaaeekikesdlvllQlEipletveealkiakkagvkvllnPAPae 165
                                                             n  lt+e++++  + i+++d++++QlE+p ++v +alk  ++ g++v+lnPAPa+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908 114 NGALTAETIDRFDSVIRAADVLICQLEVPDASVGHALKRGRELGKTVILNPAPAS 168
                                                             ******************************************************* PP

                                               TIGR02152 166 kkldeellslvdiivpNetEaeiLtgievedledaekaaekllekgvkaviitlG 220
                                                             + l++++++ +d+++pNe+Ea++L+g +v++l++a++aa++l + g+ +viitlG
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908 169 RPLPSDWYASIDYLIPNESEASALSGLSVDSLDTAQAAATRLIALGAGKVIITLG 223
                                                             ******************************************************* PP

                                               TIGR02152 221 skGallvskdekklipalkvkavDttaAGDtFigalavaLaegksledavrfana 275
                                                             ++G+l+++ ++ +++pa  vkavDttaAGDtF+g++a+aLa+g++ ++a+rf++ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908 224 AQGSLFADGQRFEHFPAPVVKAVDTTAAGDTFVGGFAAALAAGNDEAQAIRFGQV 278
                                                             ******************************************************* PP

                                               TIGR02152 276 aaalsVtrkGaqssiPtkeeve 297
                                                             aaalsVtr+Gaq+siP++++v+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3908 279 AAALSVTRAGAQPSIPALSDVQ 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 6.76
//
[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