Alignments for a candidate for rbsK in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsK in Pseudomonas fluorescens FW300-N1B4

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate Pf1N1B4_6031 Ribokinase (EC 2.7.1.15)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6031
          Length = 305

 Score =  583 bits (1503), Expect = e-171
 Identities = 305/305 (100%), Positives = 305/305 (100%)

Query: 1   MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGKSFATVSGGKGANQAVAAARLGAQVSMVG 60
           MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGKSFATVSGGKGANQAVAAARLGAQVSMVG
Sbjct: 1   MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGKSFATVSGGKGANQAVAAARLGAQVSMVG 60

Query: 61  CVGNDAYGEALRGALLAEQIDCQAVSTVEDSSGVALIVVDDNSQNAIVIVAGANGALTPE 120
           CVGNDAYGEALRGALLAEQIDCQAVSTVEDSSGVALIVVDDNSQNAIVIVAGANGALTPE
Sbjct: 61  CVGNDAYGEALRGALLAEQIDCQAVSTVEDSSGVALIVVDDNSQNAIVIVAGANGALTPE 120

Query: 121 VIDRFDAVLQAADVIICQLEVPDATVGHALKRGRELGKTVILNPAPASRPLPVDWYAAID 180
           VIDRFDAVLQAADVIICQLEVPDATVGHALKRGRELGKTVILNPAPASRPLPVDWYAAID
Sbjct: 121 VIDRFDAVLQAADVIICQLEVPDATVGHALKRGRELGKTVILNPAPASRPLPVDWYAAID 180

Query: 181 YLIPNESEASVLSGLPVDSLSTAETAATRLIAMGAGKVIITLGSQGSLFADGQRFEHFPA 240
           YLIPNESEASVLSGLPVDSLSTAETAATRLIAMGAGKVIITLGSQGSLFADGQRFEHFPA
Sbjct: 181 YLIPNESEASVLSGLPVDSLSTAETAATRLIAMGAGKVIITLGSQGSLFADGQRFEHFPA 240

Query: 241 AKVKAVDTTAAGDTFVGGFAAALAAGKGEADAIRFGQVAAALSVTRAGAQPSIPTLSDVQ 300
           AKVKAVDTTAAGDTFVGGFAAALAAGKGEADAIRFGQVAAALSVTRAGAQPSIPTLSDVQ
Sbjct: 241 AKVKAVDTTAAGDTFVGGFAAALAAGKGEADAIRFGQVAAALSVTRAGAQPSIPTLSDVQ 300

Query: 301 AFKAP 305
           AFKAP
Sbjct: 301 AFKAP 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: 445
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 Pf1N1B4_6031 (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.26865.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   4.6e-117  376.6   4.4   5.1e-117  376.4   4.4    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6031  Ribokinase (EC 2.7.1.15)


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6031  Ribokinase (EC 2.7.1.15)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  376.4   4.4  5.1e-117  5.1e-117       1     297 [.       5     300 ..       5     301 .. 0.99

  Alignments for each domain:
  == domain 1  score: 376.4 bits;  conditional E-value: 5.1e-117
                                      TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefg 64 
                                                    +vv+GS+n+Dlv+r++rlp+ Get+ +++f +++GGKGANQAvaaarlga+vsm+g+vG+D++g
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6031   5 VVVIGSLNMDLVTRAPRLPRGGETLIGKSFATVSGGKGANQAVAAARLGAQVSMVGCVGNDAYG 68 
                                                    79************************************************************** PP

                                      TIGR02152  65 eellenlkkegidteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekike 128
                                                    e+l+ +l +e+id++ v++v++ s+GvAli+vd++++N+Iv+vaGan  ltpe++++  + +++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6031  69 EALRGALLAEQIDCQAVSTVED-SSGVALIVVDDNSQNAIVIVAGANGALTPEVIDRFDAVLQA 131
                                                    ******************9965.67*************************************** PP

                                      TIGR02152 129 sdlvllQlEipletveealkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgi 192
                                                    +d++++QlE+p +tv +alk  ++ g++v+lnPAPa++ l+ ++++++d+++pNe+Ea++L+g 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6031 132 ADVIICQLEVPDATVGHALKRGRELGKTVILNPAPASRPLPVDWYAAIDYLIPNESEASVLSGL 195
                                                    **************************************************************** PP

                                      TIGR02152 193 evedledaekaaekllekgvkaviitlGskGallvskdekklipalkvkavDttaAGDtFigal 256
                                                     v++l++ae+aa++l ++g+ +viitlGs+G+l+++ ++ +++pa kvkavDttaAGDtF+g++
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6031 196 PVDSLSTAETAATRLIAMGAGKVIITLGSQGSLFADGQRFEHFPAAKVKAVDTTAAGDTFVGGF 259
                                                    **************************************************************** PP

                                      TIGR02152 257 avaLaegksledavrfanaaaalsVtrkGaqssiPtkeeve 297
                                                    a+aLa+gk  +da+rf++ aaalsVtr+Gaq+siPt+++v+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6031 260 AAALAAGKGEADAIRFGQVAAALSVTRAGAQPSIPTLSDVQ 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: 00:00:00.00
# Mc/sec: 9.99
//
[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