GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoC in Rhodobacter ovatus JA234

Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate WP_097030588.1 CRO07_RS10010 deoxyribose-phosphate aldolase

Query= BRENDA::Q9Y315
         (318 letters)



>NCBI__GCF_900207575.1:WP_097030588.1
          Length = 307

 Score =  357 bits (917), Expect = e-103
 Identities = 183/308 (59%), Positives = 235/308 (76%), Gaps = 4/308 (1%)

Query: 10  LDLSWISKIQVNHPAVLRRAEQIQARRTVKKEWQAAWLLKAVTFIDLTTLSGDDTSSNIQ 69
           LDL W+++ Q N PA+ RRA  + A R VKK+ QAAWL KA++ IDLT LSGDDT   ++
Sbjct: 3   LDLEWVAQAQANAPAIARRAASLPATRGVKKDHQAAWLCKAISLIDLTALSGDDTPGRVR 62

Query: 70  RLCYKAKYPIREDLLKALNMHDKGITTAAVCVYPARVCDAVKALKAAGCNIPVASVAAGF 129
           RLC KA+ P+R DLL AL M  +G+TT AVCVY   V  AV+AL  +G  IPVA+V+ GF
Sbjct: 63  RLCAKARQPVRPDLLAALGM--EGLTTGAVCVYHEMVETAVRALDGSG--IPVAAVSTGF 118

Query: 130 PAGQTHLKTRLEEIRLAVEDGATEIDVVINRSLVLTGQWEALYDEIRQFRKACGEAHLKT 189
           PAG +  + RL EI  +V  GA+EID+VI+R  VLTG W+ALYDE+ Q R+A G AH+K 
Sbjct: 119 PAGLSPYRLRLAEIGESVAAGASEIDIVISRRHVLTGDWQALYDEMCQMRQAAGSAHVKA 178

Query: 190 ILATGELGTLTNVYKASMIAMMAGSDFIKTSTGKETVNATFPVAIVMLRAIRDFFWKTGN 249
           ILATGELG+L NV +AS++ MMAG+DFIKTSTGKE VNAT PV++ M+RAIRD+  +TG 
Sbjct: 179 ILATGELGSLRNVARASLVCMMAGADFIKTSTGKEPVNATLPVSLTMIRAIRDYQDRTGF 238

Query: 250 KIGFKPAGGIRSAKDSLAWLSLVKEELGDEWLKPELFRIGASTLLSDIERQIYHHVTGRY 309
           +IGFKPAGGI  AK++L +L+++KEELG  WL+P+LFR GAS+LL DIERQ+ HHVTG Y
Sbjct: 239 RIGFKPAGGISKAKEALVYLAMMKEELGHPWLQPDLFRFGASSLLGDIERQLDHHVTGCY 298

Query: 310 AAYHDLPM 317
           +A +  P+
Sbjct: 299 SAANRHPL 306


Lambda     K      H
   0.320    0.133    0.397 

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: 326
Number of extensions: 12
Number of successful extensions: 3
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: 318
Length of database: 307
Length adjustment: 27
Effective length of query: 291
Effective length of database: 280
Effective search space:    81480
Effective search space used:    81480
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate WP_097030588.1 CRO07_RS10010 (deoxyribose-phosphate aldolase)
to HMM TIGR00126 (deoC: deoxyribose-phosphate aldolase (EC 4.1.2.4))

# 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/TIGR00126.hmm
# target sequence database:        /tmp/gapView.3430743.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00126  [M=211]
Accession:   TIGR00126
Description: deoC: deoxyribose-phosphate aldolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
      3e-45  140.3   0.0    5.7e-45  139.4   0.0    1.4  1  NCBI__GCF_900207575.1:WP_097030588.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900207575.1:WP_097030588.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.4   0.0   5.7e-45   5.7e-45       3     203 ..      44     267 ..      42     271 .. 0.94

  Alignments for each domain:
  == domain 1  score: 139.4 bits;  conditional E-value: 5.7e-45
                             TIGR00126   3 akliDhtalkadtteedietlcaeAkky..............kfaavcvnpsyvslAkelLkgteveictv.v 60 
                                            +liD+tal+ d+t+  + +lca+A ++               + avcv+ ++v+ A++ L g+ + +++v +
  NCBI__GCF_900207575.1:WP_097030588.1  44 ISLIDLTALSGDDTPGRVRRLCAKARQPvrpdllaalgmeglTTGAVCVYHEMVETAVRALDGSGIPVAAVsT 116
                                           689**********************99888888888877777788*************************978 PP

                             TIGR00126  61 gFPlGasttevkllEakeaieeGAdEvDvviniaalkdkneevviedikavveacakvllKvilEtalLtdee 133
                                           gFP+G s  + +l+E  e++++GA E+D+vi  + +  +++++ ++++  + +a++ +++K+il t++L    
  NCBI__GCF_900207575.1:WP_097030588.1 117 GFPAGLSPYRLRLAEIGESVAAGASEIDIVISRRHVLTGDWQALYDEMCQMRQAAGSAHVKAILATGELGSLR 189
                                           *********************************************************************9876 PP

                             TIGR00126 134 kk.kAseisieagadfvKtstgfsakgAtvedvrlmkkvvgd.......evgvKasGGvrtaedalalieaga 198
                                            + +As +++ agadf+Ktstg+  ++At+     m ++++d       ++g+K++GG+  a++al ++++  
  NCBI__GCF_900207575.1:WP_097030588.1 190 NVaRASLVCMMAGADFIKTSTGKEPVNATLPVSLTMIRAIRDyqdrtgfRIGFKPAGGISKAKEALVYLAMMK 262
                                           665***************************988889999999999************************9999 PP

                             TIGR00126 199 eriga 203
                                           e +g 
  NCBI__GCF_900207575.1:WP_097030588.1 263 EELGH 267
                                           98886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (211 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 11.10
//
[ok]

This GapMind analysis is from Sep 24 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