GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsK in Paraburkholderia bryophila 376MFSha3.1

Align deoxyribose kinase (EC 2.7.1.15) (characterized)
to candidate H281DRAFT_01116 H281DRAFT_01116 ribokinase

Query= reanno::Burk376:H281DRAFT_01116
         (320 letters)



>FitnessBrowser__Burk376:H281DRAFT_01116
          Length = 320

 Score =  618 bits (1593), Expect = 0.0
 Identities = 320/320 (100%), Positives = 320/320 (100%)

Query: 1   MSSQPQQSGRVVILGIYVTDLTFRAARMPLVGETIAGSAFAMGPGGKGSNQAVAAARAGA 60
           MSSQPQQSGRVVILGIYVTDLTFRAARMPLVGETIAGSAFAMGPGGKGSNQAVAAARAGA
Sbjct: 1   MSSQPQQSGRVVILGIYVTDLTFRAARMPLVGETIAGSAFAMGPGGKGSNQAVAAARAGA 60

Query: 61  EVVFCTRIGNDAFGSIAQATWAREGITARASVVEGVSTGAAHIFVDDTTGMNAIIVAAGA 120
           EVVFCTRIGNDAFGSIAQATWAREGITARASVVEGVSTGAAHIFVDDTTGMNAIIVAAGA
Sbjct: 61  EVVFCTRIGNDAFGSIAQATWAREGITARASVVEGVSTGAAHIFVDDTTGMNAIIVAAGA 120

Query: 121 AGTLSAADVDAIEADIAGSRVFVTQLEQPLAAARRGLEVARKHGVTTVFNPAPALPLDDD 180
           AGTLSAADVDAIEADIAGSRVFVTQLEQPLAAARRGLEVARKHGVTTVFNPAPALPLDDD
Sbjct: 121 AGTLSAADVDAIEADIAGSRVFVTQLEQPLAAARRGLEVARKHGVTTVFNPAPALPLDDD 180

Query: 181 IFPLCDYITPNETEAAALTGVPIANVDDARRAADVLLAKGVGTVIVTLGEGGALLHDATQ 240
           IFPLCDYITPNETEAAALTGVPIANVDDARRAADVLLAKGVGTVIVTLGEGGALLHDATQ
Sbjct: 181 IFPLCDYITPNETEAAALTGVPIANVDDARRAADVLLAKGVGTVIVTLGEGGALLHDATQ 240

Query: 241 SIWLPAFRCGAVVETAGAGDGFTGGFAAALARGEDAISAMRFGCALAGISVTRAGTAPSM 300
           SIWLPAFRCGAVVETAGAGDGFTGGFAAALARGEDAISAMRFGCALAGISVTRAGTAPSM
Sbjct: 241 SIWLPAFRCGAVVETAGAGDGFTGGFAAALARGEDAISAMRFGCALAGISVTRAGTAPSM 300

Query: 301 PTLAEVNRVLSESAQPAQAS 320
           PTLAEVNRVLSESAQPAQAS
Sbjct: 301 PTLAEVNRVLSESAQPAQAS 320


Lambda     K      H
   0.318    0.132    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: 436
Number of extensions: 8
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: 320
Length of database: 320
Length adjustment: 28
Effective length of query: 292
Effective length of database: 292
Effective search space:    85264
Effective search space used:    85264
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 H281DRAFT_01116 H281DRAFT_01116 (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.6398.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    3.2e-95  304.8   4.3    3.6e-95  304.7   4.3    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_01116  H281DRAFT_01116 ribokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_01116  H281DRAFT_01116 ribokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.7   4.3   3.6e-95   3.6e-95       1     297 [.      11     307 ..      11     308 .. 0.97

  Alignments for each domain:
  == domain 1  score: 304.7 bits;  conditional E-value: 3.6e-95
                                    TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgee 66 
                                                  +v++G + +Dl++r+ r+p  Get++++ f +++GGKG+NQAvaaar gaev + +++G+D+fg+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_01116  11 VVILGIYVTDLTFRAARMPLVGETIAGSAFAMGPGGKGSNQAVAAARAGAEVVFCTRIGNDAFGSI 76 
                                                  799*************************************************************** PP

                                    TIGR02152  67 llenlkkegidteyvkkvkktstGvAlilvde.egeNsIvvvaGaneeltpedvkaaeekikesdl 131
                                                  +  ++++egi t   + v+ +stG A+i+vd+ +g N+I+v+aGa  +l+++dv+a e++i+ s++
  lcl|FitnessBrowser__Burk376:H281DRAFT_01116  77 AQATWAREGI-TARASVVEGVSTGAAHIFVDDtTGMNAIIVAAGAAGTLSAADVDAIEADIAGSRV 141
                                                  **********.7778899************983589****************************** PP

                                    TIGR02152 132 vllQlEipletveealkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedl 197
                                                   + QlE pl+++++ l++a+k+gv++++nPAPa + ld++++ l+d+i+pNetEa++Ltg+ ++++
  lcl|FitnessBrowser__Burk376:H281DRAFT_01116 142 FVTQLEQPLAAARRGLEVARKHGVTTVFNPAPALP-LDDDIFPLCDYITPNETEAAALTGVPIANV 206
                                                  *********************************76.99**************************** PP

                                    TIGR02152 198 edaekaaekllekgvkaviitlGskGallvskdekklipalkvka.vDttaAGDtFigalavaLae 262
                                                  +da++aa+ ll+kgv +vi+tlG+ Gall++++++  +pa++  a v t++AGD F+g++a+aLa+
  lcl|FitnessBrowser__Burk376:H281DRAFT_01116 207 DDARRAADVLLAKGVGTVIVTLGEGGALLHDATQSIWLPAFRCGAvVETAGAGDGFTGGFAAALAR 272
                                                  ******************************************97626999**************** PP

                                    TIGR02152 263 gksledavrfanaaaalsVtrkGaqssiPtkeeve 297
                                                  g+++ +a+rf+ a+a +sVtr+G+++s+Pt++ev+
  lcl|FitnessBrowser__Burk376:H281DRAFT_01116 273 GEDAISAMRFGCALAGISVTRAGTAPSMPTLAEVN 307
                                                  *********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (320 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: 00:00:00.01
# Mc/sec: 7.23
//
[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