GapMind for catabolism of small carbon sources

 

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

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate H281DRAFT_05229 H281DRAFT_05229 ribokinase

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



>FitnessBrowser__Burk376:H281DRAFT_05229
          Length = 307

 Score =  368 bits (945), Expect = e-107
 Identities = 200/299 (66%), Positives = 232/299 (77%), Gaps = 1/299 (0%)

Query: 3   AKVVVVGSLNMDLVTRAQRLPHAGETLHGESFATVSGGKGANQAVASARLGAQVSMIGCV 62
           A+V VVGSLNMDLV RA RLPH GETL G +FA V+GGKG NQAVA+ARLGAQVSM+GCV
Sbjct: 8   ARVAVVGSLNMDLVARAPRLPHPGETLAGRTFAQVAGGKGGNQAVAAARLGAQVSMLGCV 67

Query: 63  GDDAYGEQLRAALLAEQIDCQALTSVEGSSGVALIVVDDNSQNAIVIVAGANGQLTPGMV 122
           G DA G QLRA L AE IDC A+ +   ++GVALIVVDD SQNAIVIVAG+NG++TP  +
Sbjct: 68  GADANGAQLRAGLEAEGIDCAAVETGREATGVALIVVDDASQNAIVIVAGSNGEVTPETI 127

Query: 123 AGFDAVLAAADVIICQLEVPMHTVGYVLKRGRELGKTVILNPAPATSPLPADWYSSIDYL 182
           A  +AVLAAADV+ICQLE P+ TV   L   R LGKTVILNPAPAT PLPA+W   IDYL
Sbjct: 128 ARHEAVLAAADVVICQLETPLDTVQAALATARRLGKTVILNPAPATGPLPAEWLPLIDYL 187

Query: 183 IPNESEASALSGLPVDSLESAELAASRLIAAGAGKVIITLGPQGSLFA-NGQSCEHFPAP 241
           IPNE EA+ L+GLPV S E A  AA+ L AAGA  V++TLGP+G   A  G +   + AP
Sbjct: 188 IPNELEAATLTGLPVGSPEEAATAAAVLRAAGARNVLVTLGPRGVQAALEGAAPALYDAP 247

Query: 242 KVKSVDTTAAGDTFVGGFAAALAAGKSEVEAIRFGQVAAALSVTRAGAQPSIPSLSDVQ 300
           KVK++DTTAAGDTF+GGFAA LA G S   AIRF Q AAALSVTRAGAQPSIP+ ++V+
Sbjct: 248 KVKAIDTTAAGDTFIGGFAAQLAQGASVDAAIRFAQRAAALSVTRAGAQPSIPTWTEVE 306


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: 323
Number of extensions: 11
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: 307
Length adjustment: 27
Effective length of query: 278
Effective length of database: 280
Effective search space:    77840
Effective search space used:    77840
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 H281DRAFT_05229 H281DRAFT_05229 (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.3587.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   5.8e-112  359.8   5.4   6.5e-112  359.7   5.4    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05229  H281DRAFT_05229 ribokinase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05229  H281DRAFT_05229 ribokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  359.7   5.4  6.5e-112  6.5e-112       1     297 [.      10     306 ..      10     307 .] 0.98

  Alignments for each domain:
  == domain 1  score: 359.7 bits;  conditional E-value: 6.5e-112
                                    TIGR02152   1 ivvvGSinvDlvlrvkrlpkpGetvkaeefkiaaGGKGANQAvaaarlgaevsmigkvGkDefgee 66 
                                                  ++vvGS+n+Dlv+r++rlp+pGet+++++f ++aGGKG NQAvaaarlga+vsm+g+vG D+ g++
  lcl|FitnessBrowser__Burk376:H281DRAFT_05229  10 VAVVGSLNMDLVARAPRLPHPGETLAGRTFAQVAGGKGGNQAVAAARLGAQVSMLGCVGADANGAQ 75 
                                                  78**************************************************************** PP

                                    TIGR02152  67 llenlkkegidteyvkkvkktstGvAlilvdeegeNsIvvvaGaneeltpedvkaaeekikesdlv 132
                                                  l+  l++egid+  v++  +++tGvAli+vd+ ++N+Iv+vaG+n e+tpe+++++e+ ++++d+v
  lcl|FitnessBrowser__Burk376:H281DRAFT_05229  76 LRAGLEAEGIDCAAVETG-REATGVALIVVDDASQNAIVIVAGSNGEVTPETIARHEAVLAAADVV 140
                                                  ***************965.7889******************************************* PP

                                    TIGR02152 133 llQlEipletveealkiakkagvkvllnPAPaekkldeellslvdiivpNetEaeiLtgievedle 198
                                                  ++QlE+pl+tv++al +a++ g++v+lnPAPa+  l++e+l l+d+++pNe Ea++Ltg  v + e
  lcl|FitnessBrowser__Burk376:H281DRAFT_05229 141 ICQLETPLDTVQAALATARRLGKTVILNPAPATGPLPAEWLPLIDYLIPNELEAATLTGLPVGSPE 206
                                                  ****************************************************************** PP

                                    TIGR02152 199 daekaaekllekgvkaviitlGskGallvskd.ekklipalkvkavDttaAGDtFigalavaLaeg 263
                                                  +a +aa+ l++ g+++v++tlG +G+  + ++   +l +a kvka+DttaAGDtFig++a++La+g
  lcl|FitnessBrowser__Burk376:H281DRAFT_05229 207 EAATAAAVLRAAGARNVLVTLGPRGVQAALEGaAPALYDAPKVKAIDTTAAGDTFIGGFAAQLAQG 272
                                                  **************************9988876899****************************** PP

                                    TIGR02152 264 ksledavrfanaaaalsVtrkGaqssiPtkeeve 297
                                                   s+++a+rfa++aaalsVtr+Gaq+siPt +eve
  lcl|FitnessBrowser__Burk376:H281DRAFT_05229 273 ASVDAAIRFAQRAAALSVTRAGAQPSIPTWTEVE 306
                                                  ********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (298 nodes)
Target sequences:                          1  (307 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: 7.32
//
[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