Alignments for a candidate for deoC in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoC in Phaeobacter inhibens BS107

Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate GFF3226 PGA1_c32790 putative deoxyribose-phosphate aldolase

Query= BRENDA::Q9Y315
         (318 letters)



>FitnessBrowser__Phaeo:GFF3226
          Length = 329

 Score =  371 bits (953), Expect = e-107
 Identities = 188/307 (61%), Positives = 234/307 (76%), Gaps = 4/307 (1%)

Query: 5   NRGTELDLSWISKIQVNHPAVLRRAEQIQARRTVKKEWQAAWLLKAVTFIDLTTLSGDDT 64
           N G ELDL W   ++ N  A+ RR   +  RR+VKK  QAAWLLKA+T IDLTTLSGDDT
Sbjct: 20  NPGMELDLDWALGVEANTSAIERRCATLPGRRSVKKNHQAAWLLKAITLIDLTTLSGDDT 79

Query: 65  SSNIQRLCYKAKYPIREDLLKALNMHDKGITTAAVCVYPARVCDAVKALKAAGCNIPVAS 124
              +QRLC KA+ P+R DL++AL+M    ITT AVCVY   +  AV AL   G  IPVA+
Sbjct: 80  VGRVQRLCAKARQPVRADLMQALDMEP--ITTGAVCVYHDMIETAVAALDGTG--IPVAA 135

Query: 125 VAAGFPAGQTHLKTRLEEIRLAVEDGATEIDVVINRSLVLTGQWEALYDEIRQFRKACGE 184
           V+ GFP G +    RL EI  +V+ GA EID+VI+R  VL+G W+ALYDE++ FR+ACG+
Sbjct: 136 VSTGFPGGLSPFHLRLAEIEESVKAGAKEIDIVISRRHVLSGNWQALYDEMKAFREACGD 195

Query: 185 AHLKTILATGELGTLTNVYKASMIAMMAGSDFIKTSTGKETVNATFPVAIVMLRAIRDFF 244
           AH+K ILATGELGTL NV +AS+I MMAG+DFIKTSTGKE+VNAT PV++VM+R IRD+ 
Sbjct: 196 AHVKAILATGELGTLRNVARASLICMMAGADFIKTSTGKESVNATLPVSLVMIRTIRDYH 255

Query: 245 WKTGNKIGFKPAGGIRSAKDSLAWLSLVKEELGDEWLKPELFRIGASTLLSDIERQIYHH 304
            +TG ++G+KPAGGI  AKDSL +LSL+KEELGD WL+P+LFR GAS+LL DIERQ+ HH
Sbjct: 256 ERTGYRVGYKPAGGISKAKDSLVYLSLIKEELGDRWLQPDLFRFGASSLLGDIERQLEHH 315

Query: 305 VTGRYAA 311
           VTG Y+A
Sbjct: 316 VTGAYSA 322


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: 339
Number of extensions: 10
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: 329
Length adjustment: 28
Effective length of query: 290
Effective length of database: 301
Effective search space:    87290
Effective search space used:    87290
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 GFF3226 PGA1_c32790 (putative 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.29606.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
    6.8e-49  152.2   0.0    1.5e-48  151.1   0.0    1.5  1  lcl|FitnessBrowser__Phaeo:GFF3226  PGA1_c32790 putative deoxyribose


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF3226  PGA1_c32790 putative deoxyribose-phosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.1   0.0   1.5e-48   1.5e-48       3     203 ..      66     289 ..      64     293 .. 0.93

  Alignments for each domain:
  == domain 1  score: 151.1 bits;  conditional E-value: 1.5e-48
                          TIGR00126   3 akliDhtalkadtteedietlcaeAkky..............kfaavcvnpsyvslAkelLkgteveictv.vgFP 63 
                                         +liD+t+l+ d+t   +++lca+A ++               + avcv+  +++ A+  L gt + +++v +gFP
  lcl|FitnessBrowser__Phaeo:GFF3226  66 ITLIDLTTLSGDDTVGRVQRLCAKARQPvradlmqaldmepiTTGAVCVYHDMIETAVAALDGTGIPVAAVsTGFP 141
                                        679**********************99887777777777777788*************************978*** PP

                          TIGR00126  64 lGasttevkllEakeaieeGAdEvDvviniaalkdkneevviedikavveacakvllKvilEtalLtd.eekkkAs 138
                                         G s  + +l+E +e++++GA+E+D+vi  + + ++n+++ ++++ka  eac+++++K+il t++L    ++ +As
  lcl|FitnessBrowser__Phaeo:GFF3226 142 GGLSPFHLRLAEIEESVKAGAKEIDIVISRRHVLSGNWQALYDEMKAFREACGDAHVKAILATGELGTlRNVARAS 217
                                        ******************************************************************6615666*** PP

                          TIGR00126 139 eisieagadfvKtstgfsakgAtvedvrlmkkvvgd.......evgvKasGGvrtaedalalieagaeriga 203
                                         i++ agadf+Ktstg+  ++At+    +m ++++d       +vg K++GG+  a+d l +++   e +g 
  lcl|FitnessBrowser__Phaeo:GFF3226 218 LICMMAGADFIKTSTGKESVNATLPVSLVMIRTIRDyhertgyRVGYKPAGGISKAKDSLVYLSLIKEELGD 289
                                        *************************99*********************************999988888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (211 nodes)
Target sequences:                          1  (329 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 0.00s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 3.63
//
[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