Aligments for a candidate for deoK in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Aligments for a candidate for deoK in Pseudomonas fluorescens FW300-N2C3

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate AO356_00950 AO356_00950 ribokinase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_00950
          Length = 304

 Score =  584 bits (1505), Expect = e-171
 Identities = 304/304 (100%), Positives = 304/304 (100%)

Query: 1   MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGESFATIPGGKGANQAVAAARLGAQVSMVG 60
           MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGESFATIPGGKGANQAVAAARLGAQVSMVG
Sbjct: 1   MPAKVVVIGSLNMDLVTRAPRLPRGGETLIGESFATIPGGKGANQAVAAARLGAQVSMVG 60

Query: 61  CVGDDAYGEQLRGALLAEGIDCQAVRVEQGSSGVALIVVDDNSQNAIVIVAGANGALTAE 120
           CVGDDAYGEQLRGALLAEGIDCQAVRVEQGSSGVALIVVDDNSQNAIVIVAGANGALTAE
Sbjct: 61  CVGDDAYGEQLRGALLAEGIDCQAVRVEQGSSGVALIVVDDNSQNAIVIVAGANGALTAE 120

Query: 121 VLDGVDDVLQSADVIICQLEVPDATVGHALKRGRALGKIVILNPAPASHALPADWYACID 180
           VLDGVDDVLQSADVIICQLEVPDATVGHALKRGRALGKIVILNPAPASHALPADWYACID
Sbjct: 121 VLDGVDDVLQSADVIICQLEVPDATVGHALKRGRALGKIVILNPAPASHALPADWYACID 180

Query: 181 YLIPNESEAAVLSGLAVDSLETAEAAAAHLIAAGAGKVIVTLGAQGLMFANGASFEHFPA 240
           YLIPNESEAAVLSGLAVDSLETAEAAAAHLIAAGAGKVIVTLGAQGLMFANGASFEHFPA
Sbjct: 181 YLIPNESEAAVLSGLAVDSLETAEAAAAHLIAAGAGKVIVTLGAQGLMFANGASFEHFPA 240

Query: 241 PRVKAVDTTAAGDTFVGGFAAALACGKSEVDAIRFGQVAAALSVTRAGAQPSIPTLLEVQ 300
           PRVKAVDTTAAGDTFVGGFAAALACGKSEVDAIRFGQVAAALSVTRAGAQPSIPTLLEVQ
Sbjct: 241 PRVKAVDTTAAGDTFVGGFAAALACGKSEVDAIRFGQVAAALSVTRAGAQPSIPTLLEVQ 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: 502
Number of extensions: 14
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: 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 AO356_00950 AO356_00950 (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.7727.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   6.2e-115  369.6   5.3   6.9e-115  369.4   5.3    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00950  AO356_00950 ribokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00950  AO356_00950 ribokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.4   5.3  6.9e-115  6.9e-115       1     297 [.       5     300 ..       5     301 .. 0.99

  Alignments for each domain:
  == domain 1  score: 369.4 bits;  conditional E-value: 6.9e-115
                                       TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDef 63 
                                                     +vv+GS+n+Dlv+r++rlp+ Get+ +e+f +++GGKGANQAvaaarlga+vsm+g+vG+D++
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00950   5 VVVIGSLNMDLVTRAPRLPRGGETLIGESFATIPGGKGANQAVAAARLGAQVSMVGCVGDDAY 67 
                                                     79************************************************************* PP

                                       TIGR02152  64 geellenlkkegidteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeeki 126
                                                     ge+l+ +l +egid++ v+ v++ s+GvAli+vd++++N+Iv+vaGan  lt+e+++   + +
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00950  68 GEQLRGALLAEGIDCQAVR-VEQGSSGVALIVVDDNSQNAIVIVAGANGALTAEVLDGVDDVL 129
                                                     ******************9.668899************************************* PP

                                       TIGR02152 127 kesdlvllQlEipletveealkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiL 189
                                                     +++d++++QlE+p +tv +alk  ++ g+ v+lnPAPa+++l++++++ +d+++pNe+Ea++L
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00950 130 QSADVIICQLEVPDATVGHALKRGRALGKIVILNPAPASHALPADWYACIDYLIPNESEAAVL 192
                                                     *************************************************************** PP

                                       TIGR02152 190 tgievedledaekaaekllekgvkaviitlGskGallvskdekklipalkvkavDttaAGDtF 252
                                                     +g +v++le+ae+aa++l + g+ +vi+tlG++G ++++  + +++pa +vkavDttaAGDtF
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00950 193 SGLAVDSLETAEAAAAHLIAAGAGKVIVTLGAQGLMFANGASFEHFPAPRVKAVDTTAAGDTF 255
                                                     *************************************************************** PP

                                       TIGR02152 253 igalavaLaegksledavrfanaaaalsVtrkGaqssiPtkeeve 297
                                                     +g++a+aLa gks  da+rf++ aaalsVtr+Gaq+siPt+ ev+
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_00950 256 VGGFAAALACGKSEVDAIRFGQVAAALSVTRAGAQPSIPTLLEVQ 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.55
//
[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, or view the source code.

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