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

GapMind for catabolism of small carbon sources

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

Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate H281DRAFT_01118 H281DRAFT_01118 deoxyribose-phosphate aldolase

Query= BRENDA::Q9Y315
         (318 letters)



>FitnessBrowser__Burk376:H281DRAFT_01118
          Length = 337

 Score =  370 bits (951), Expect = e-107
 Identities = 187/314 (59%), Positives = 238/314 (75%), Gaps = 2/314 (0%)

Query: 5   NRGTELDLSWISKIQVNHPAVLRRAEQIQARRTVKKEWQAAWLLKAVTFIDLTTLSGDDT 64
           N G   D SW+  +++N  AV RR   +  RRTVKK+ QAAWLLKAVT IDLTTLSGDDT
Sbjct: 26  NPGMPFDASWLDGLRINQSAVERRTATLATRRTVKKDAQAAWLLKAVTCIDLTTLSGDDT 85

Query: 65  SSNIQRLCYKAKYPIREDLLKALNMHDKGITTAAVCVYPARVCDAVKALKAAGCNIPVAS 124
              ++RLC KA+ P+R DLL+AL M  + +TT AVCVY   V  AV ALK +G  IPVA+
Sbjct: 86  EGRVRRLCAKARQPVRADLLEALGMTPQRVTTGAVCVYHRFVAAAVDALKGSG--IPVAA 143

Query: 125 VAAGFPAGQTHLKTRLEEIRLAVEDGATEIDVVINRSLVLTGQWEALYDEIRQFRKACGE 184
           V+ GFPAG      +L+EI  +V DGA EID+V+ R  VLTG W+ALYDE+R+FR ACG 
Sbjct: 144 VSTGFPAGLIPHPLKLKEIEASVADGAAEIDIVVTREYVLTGNWQALYDEVREFRAACGP 203

Query: 185 AHLKTILATGELGTLTNVYKASMIAMMAGSDFIKTSTGKETVNATFPVAIVMLRAIRDFF 244
           AHLK ILATG++ TL+N+ +ASM+ MMAG+DFIKTSTGKE VNAT  V++VM+R IR++ 
Sbjct: 204 AHLKAILATGDIRTLSNIARASMVCMMAGADFIKTSTGKEGVNATLDVSLVMVRMIREYH 263

Query: 245 WKTGNKIGFKPAGGIRSAKDSLAWLSLVKEELGDEWLKPELFRIGASTLLSDIERQIYHH 304
            +TG  IGFKPAGG+ SAK  L++  L+KEELG  WL+PELFRIGAS+LL+DIERQ+ HH
Sbjct: 264 ERTGVPIGFKPAGGVSSAKSVLSYQILMKEELGRAWLEPELFRIGASSLLADIERQLEHH 323

Query: 305 VTGRYAAYHDLPMS 318
           V+GRY+A++  P++
Sbjct: 324 VSGRYSAFNRHPVA 337


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: 336
Number of extensions: 9
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: 337
Length adjustment: 28
Effective length of query: 290
Effective length of database: 309
Effective search space:    89610
Effective search space used:    89610
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 H281DRAFT_01118 H281DRAFT_01118 (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.24267.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
    2.2e-44  137.5   0.1    1.2e-43  135.0   0.1    1.8  1  lcl|FitnessBrowser__Burk376:H281DRAFT_01118  H281DRAFT_01118 deoxyribose-phos


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_01118  H281DRAFT_01118 deoxyribose-phosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.0   0.1   1.2e-43   1.2e-43       3     201 ..      72     295 ..      70     300 .. 0.91

  Alignments for each domain:
  == domain 1  score: 135.0 bits;  conditional E-value: 1.2e-43
                                    TIGR00126   3 akliDhtalkadtteedietlcaeAkky................kfaavcvnpsyvslAkelLkgt 52 
                                                   + iD+t+l+ d+te  + +lca+A ++                 + avcv+ ++v  A++ Lkg+
  lcl|FitnessBrowser__Burk376:H281DRAFT_01118  72 VTCIDLTTLSGDDTEGRVRRLCAKARQPvradllealgmtpqrvTTGAVCVYHRFVAAAVDALKGS 137
                                                  578**********************9987777777777777766688******************* PP

                                    TIGR00126  53 eveictv.vgFPlGasttevkllEakeaieeGAdEvDvviniaalkdkneevviedikavveacak 117
                                                   + +++v +gFP+G   +  kl E +++++ GA E+D+v+    +  +n+++ +++++    ac+ 
  lcl|FitnessBrowser__Burk376:H281DRAFT_01118 138 GIPVAAVsTGFPAGLIPHPLKLKEIEASVADGAAEIDIVVTREYVLTGNWQALYDEVREFRAACGP 203
                                                  ******978********************************************************* PP

                                    TIGR00126 118 vllKvilEtalLtd.eekkkAseisieagadfvKtstgfsakgAtvedvrlmkkvvgd.......e 175
                                                  ++lK+il t+ ++  +++ +As +++ agadf+Ktstg+  ++At++   +m +++++        
  lcl|FitnessBrowser__Burk376:H281DRAFT_01118 204 AHLKAILATGDIRTlSNIARASMVCMMAGADFIKTSTGKEGVNATLDVSLVMVRMIREyhertgvP 269
                                                  **********996527778***************************99999999999999999999 PP

                                    TIGR00126 176 vgvKasGGvrtaedalalieagaeri 201
                                                  +g+K++GGv  a+ +l++     e +
  lcl|FitnessBrowser__Burk376:H281DRAFT_01118 270 IGFKPAGGVSSAKSVLSYQILMKEEL 295
                                                  *************9998865555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (211 nodes)
Target sequences:                          1  (337 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: 3.77
//
[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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources