GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoC in Burkholderia phytofirmans PsJN

Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate BPHYT_RS25815 BPHYT_RS25815 deoxyribose-phosphate aldolase

Query= BRENDA::Q9Y315
         (318 letters)



>FitnessBrowser__BFirm:BPHYT_RS25815
          Length = 336

 Score =  364 bits (935), Expect = e-105
 Identities = 186/314 (59%), Positives = 238/314 (75%), Gaps = 2/314 (0%)

Query: 5   NRGTELDLSWISKIQVNHPAVLRRAEQIQARRTVKKEWQAAWLLKAVTFIDLTTLSGDDT 64
           N G   D SW+  ++VN  AV RR   +  RR+VKK+ QAAWLLKAVT IDLTTL+GDDT
Sbjct: 25  NPGMPFDASWLDGLRVNQSAVERRTATLGTRRSVKKDAQAAWLLKAVTCIDLTTLNGDDT 84

Query: 65  SSNIQRLCYKAKYPIREDLLKALNMHDKGITTAAVCVYPARVCDAVKALKAAGCNIPVAS 124
              ++RLC KA+ P+R DLL+AL +  +GITT AVCVY   V  AV AL  +G  IPVA+
Sbjct: 85  EGRVRRLCAKARQPVRADLLEALGLAPQGITTGAVCVYHRFVAAAVDALHGSG--IPVAA 142

Query: 125 VAAGFPAGQTHLKTRLEEIRLAVEDGATEIDVVINRSLVLTGQWEALYDEIRQFRKACGE 184
           V+ GFPAG      +L+EI  +V DGA EID+V+ R  VLTG W+ALYDE+R FR ACG 
Sbjct: 143 VSTGFPAGLIPHPLKLKEIEASVADGAQEIDIVVTREYVLTGNWQALYDEVRDFRAACGP 202

Query: 185 AHLKTILATGELGTLTNVYKASMIAMMAGSDFIKTSTGKETVNATFPVAIVMLRAIRDFF 244
           AHLKTILATG++ TL+NV +ASM+ MMAG+DFIKTSTGKE VNAT  V++VM+R IR++ 
Sbjct: 203 AHLKTILATGDIRTLSNVARASMVCMMAGADFIKTSTGKEGVNATLDVSLVMVRMIREYQ 262

Query: 245 WKTGNKIGFKPAGGIRSAKDSLAWLSLVKEELGDEWLKPELFRIGASTLLSDIERQIYHH 304
            +TG  IGFKPAGG+ +AK  L++  L+KEELG  WL+PELFRIGAS+LL+DIERQ+ H+
Sbjct: 263 ERTGVLIGFKPAGGVSTAKSVLSYQILMKEELGRAWLEPELFRIGASSLLADIERQLEHY 322

Query: 305 VTGRYAAYHDLPMS 318
           V+GRY+A++  P++
Sbjct: 323 VSGRYSAFNRHPVA 336


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: 323
Number of extensions: 8
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: 318
Length of database: 336
Length adjustment: 28
Effective length of query: 290
Effective length of database: 308
Effective search space:    89320
Effective search space used:    89320
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 BPHYT_RS25815 BPHYT_RS25815 (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.6757.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
    1.1e-44  138.4   0.1    4.7e-44  136.4   0.1    1.8  1  lcl|FitnessBrowser__BFirm:BPHYT_RS25815  BPHYT_RS25815 deoxyribose-phosph


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS25815  BPHYT_RS25815 deoxyribose-phosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.4   0.1   4.7e-44   4.7e-44       3     202 ..      71     295 ..      69     300 .. 0.92

  Alignments for each domain:
  == domain 1  score: 136.4 bits;  conditional E-value: 4.7e-44
                                TIGR00126   3 akliDhtalkadtteedietlcaeAkky................kfaavcvnpsyvslAkelLkgtevei 56 
                                               + iD+t+l+ d+te  + +lca+A ++                 + avcv+ ++v  A++ L+g+ + +
  lcl|FitnessBrowser__BFirm:BPHYT_RS25815  71 VTCIDLTTLNGDDTEGRVRRLCAKARQPvradllealglapqgiTTGAVCVYHRFVAAAVDALHGSGIPV 140
                                              578**********************9988888888887777766788*********************** PP

                                TIGR00126  57 ctv.vgFPlGasttevkllEakeaieeGAdEvDvviniaalkdkneevviedikavveacakvllKvilE 125
                                              ++v +gFP+G   +  kl E +++++ GA+E+D+v+    +  +n+++ +++++    ac+ ++lK il 
  lcl|FitnessBrowser__BFirm:BPHYT_RS25815 141 AAVsTGFPAGLIPHPLKLKEIEASVADGAQEIDIVVTREYVLTGNWQALYDEVRDFRAACGPAHLKTILA 210
                                              **978***************************************************************** PP

                                TIGR00126 126 talLtd.eekkkAseisieagadfvKtstgfsakgAtvedvrlmkkvvgd.......evgvKasGGvrta 187
                                              t+ ++  +++ +As +++ agadf+Ktstg+  ++At++   +m +++++        +g+K++GGv ta
  lcl|FitnessBrowser__BFirm:BPHYT_RS25815 211 TGDIRTlSNVARASMVCMMAGADFIKTSTGKEGVNATLDVSLVMVRMIREyqertgvLIGFKPAGGVSTA 280
                                              **997625666***************************99999999999999999999************ PP

                                TIGR00126 188 edalalieagaerig 202
                                              + +l++     e +g
  lcl|FitnessBrowser__BFirm:BPHYT_RS25815 281 KSVLSYQILMKEELG 295
                                              **9988666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (211 nodes)
Target sequences:                          1  (336 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 2.98
//
[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