GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoK in Pseudomonas fluorescens FW300-N2E3

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate AO353_20835 AO353_20835 ribokinase

Query= reanno::pseudo3_N2E3:AO353_20835
         (305 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_20835
          Length = 305

 Score =  584 bits (1506), Expect = e-172
 Identities = 305/305 (100%), Positives = 305/305 (100%)

Query: 1   MPAKVVVVGSLNMDLVTRAQRLPHAGETLHGESFATVSGGKGANQAVASARLGAQVSMIG 60
           MPAKVVVVGSLNMDLVTRAQRLPHAGETLHGESFATVSGGKGANQAVASARLGAQVSMIG
Sbjct: 1   MPAKVVVVGSLNMDLVTRAQRLPHAGETLHGESFATVSGGKGANQAVASARLGAQVSMIG 60

Query: 61  CVGDDAYGEQLRAALLAEQIDCQALTSVEGSSGVALIVVDDNSQNAIVIVAGANGQLTPG 120
           CVGDDAYGEQLRAALLAEQIDCQALTSVEGSSGVALIVVDDNSQNAIVIVAGANGQLTPG
Sbjct: 61  CVGDDAYGEQLRAALLAEQIDCQALTSVEGSSGVALIVVDDNSQNAIVIVAGANGQLTPG 120

Query: 121 MVAGFDAVLAAADVIICQLEVPMHTVGYVLKRGRELGKTVILNPAPATSPLPADWYSSID 180
           MVAGFDAVLAAADVIICQLEVPMHTVGYVLKRGRELGKTVILNPAPATSPLPADWYSSID
Sbjct: 121 MVAGFDAVLAAADVIICQLEVPMHTVGYVLKRGRELGKTVILNPAPATSPLPADWYSSID 180

Query: 181 YLIPNESEASALSGLPVDSLESAELAASRLIAAGAGKVIITLGPQGSLFANGQSCEHFPA 240
           YLIPNESEASALSGLPVDSLESAELAASRLIAAGAGKVIITLGPQGSLFANGQSCEHFPA
Sbjct: 181 YLIPNESEASALSGLPVDSLESAELAASRLIAAGAGKVIITLGPQGSLFANGQSCEHFPA 240

Query: 241 PKVKSVDTTAAGDTFVGGFAAALAAGKSEVEAIRFGQVAAALSVTRAGAQPSIPSLSDVQ 300
           PKVKSVDTTAAGDTFVGGFAAALAAGKSEVEAIRFGQVAAALSVTRAGAQPSIPSLSDVQ
Sbjct: 241 PKVKSVDTTAAGDTFVGGFAAALAAGKSEVEAIRFGQVAAALSVTRAGAQPSIPSLSDVQ 300

Query: 301 AFKAS 305
           AFKAS
Sbjct: 301 AFKAS 305


Lambda     K      H
   0.315    0.130    0.363 

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: 453
Number of extensions: 10
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 AO353_20835 AO353_20835 (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.30356.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                     -----------
   1.5e-115  371.6   2.7   1.7e-115  371.4   2.7    1.0  1  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20835  AO353_20835 ribokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo3_N2E3:AO353_20835  AO353_20835 ribokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  371.4   2.7  1.7e-115  1.7e-115       1     297 [.       5     300 ..       5     301 .. 0.99

  Alignments for each domain:
  == domain 1  score: 371.4 bits;  conditional E-value: 1.7e-115
                                     TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefge 65 
                                                   +vvvGS+n+Dlv+r++rlp++Get+++e+f +++GGKGANQAva arlga+vsmig+vG+D++ge
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20835   5 VVVVGSLNMDLVTRAQRLPHAGETLHGESFATVSGGKGANQAVASARLGAQVSMIGCVGDDAYGE 69 
                                                   79*************************************************************** PP

                                     TIGR02152  66 ellenlkkegidteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekikesd 130
                                                   +l+ +l +e+id++ +++v+  s+GvAli+vd++++N+Iv+vaGan +ltp +v+   + ++++d
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20835  70 QLRAALLAEQIDCQALTSVE-GSSGVALIVVDDNSQNAIVIVAGANGQLTPGMVAGFDAVLAAAD 133
                                                   *****************885.577***************************************** PP

                                     TIGR02152 131 lvllQlEipletveealkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgieve 195
                                                   ++++QlE+p++tv ++lk  ++ g++v+lnPAPa++ l+++++s +d+++pNe+Ea++L+g  v+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20835 134 VIICQLEVPMHTVGYVLKRGRELGKTVILNPAPATSPLPADWYSSIDYLIPNESEASALSGLPVD 198
                                                   ***************************************************************** PP

                                     TIGR02152 196 dledaekaaekllekgvkaviitlGskGallvskdekklipalkvkavDttaAGDtFigalavaL 260
                                                   +le+ae aa++l + g+ +viitlG +G+l+++ ++++++pa kvk vDttaAGDtF+g++a+aL
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20835 199 SLESAELAASRLIAAGAGKVIITLGPQGSLFANGQSCEHFPAPKVKSVDTTAAGDTFVGGFAAAL 263
                                                   ***************************************************************** PP

                                     TIGR02152 261 aegksledavrfanaaaalsVtrkGaqssiPtkeeve 297
                                                   a+gks  +a+rf++ aaalsVtr+Gaq+siP++++v+
  lcl|FitnessBrowser__pseudo3_N2E3:AO353_20835 264 AAGKSEVEAIRFGQVAAALSVTRAGAQPSIPSLSDVQ 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 7.65
//
[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:

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:

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:

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:

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