Alignments for a candidate for deoA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Phaeobacter inhibens BS107

Align thymidine phosphorylase (EC 2.4.2.4) (characterized)
to candidate GFF1179 PGA1_c11940 thymidine phosphorylase DeoA

Query= BRENDA::Q7CP66
         (440 letters)



>FitnessBrowser__Phaeo:GFF1179
          Length = 436

 Score =  392 bits (1008), Expect = e-114
 Identities = 212/437 (48%), Positives = 284/437 (64%), Gaps = 4/437 (0%)

Query: 4   AQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLTMAM 63
           A+ II   R G   SD ++R+F  G+ + T+S+ Q  A AM +    + +  R +LT+AM
Sbjct: 3   ARAIIASLRRGDTPSDADLRWFAEGLANGTVSDAQAGAFAMAVCLQGLGVEARGALTLAM 62

Query: 64  RDSGTVLDWKSLNLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYVPMISGRGLGHTGGT 123
           RDSG VL W   +L+GP++DKHSTGGVGD  SL+L P +A CG YVPMISGRGLGHTGGT
Sbjct: 63  RDSGDVLRW---DLDGPVLDKHSTGGVGDCVSLLLAPALAECGAYVPMISGRGLGHTGGT 119

Query: 124 LDKLEAIPGFDIFPDDNRFREIIQDVGVAIIGQTSSLAPADKRFYATRDITATVDSIPLI 183
           LDK+EAIPG  I   +     ++Q VG AI+G T+ +APADKR YA RD+TATVDS+ LI
Sbjct: 120 LDKMEAIPGVSIQVSEQDLVAMMQGVGCAIVGATAQIAPADKRLYAIRDVTATVDSLDLI 179

Query: 184 TGSILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTALLTDMN 243
           T SIL+KKLA   DALV+DVK+GSGAFM T E +EALA ++   AN AG RT+AL+TDMN
Sbjct: 180 TASILSKKLAASTDALVLDVKIGSGAFMKTLEEAEALALSLTETANAAGCRTSALITDMN 239

Query: 244 QVLASSAGNAVEVREAVQFLTG-EYRNPRLFDVTMALCVEMLISGQLAKDDAEARAKLQA 302
           Q LA + GNA+EV E ++ LTG   +   L ++T      +L  G LA D       ++ 
Sbjct: 240 QPLAPALGNALEVAEVMRVLTGVSGQGGALTELTAEQGGVLLAHGGLAADAEAGAEMIRK 299

Query: 303 VLDNGKAAEVFGRMVAAQKGPSDFVENYDKYLPTAMLSKAVYADTEGFISAMDTRALGMA 362
            + +G  AE F RMVAA  G SDF E +   LPTA + + +  +  G++SA+D  ALG+A
Sbjct: 300 AIASGAVAERFARMVAAMGGSSDFAETWQTILPTAPVQRRIKVEQTGYVSAIDGEALGLA 359

Query: 363 VVSMGGGRRQASDTIDYSVGFTDMARLGDSIDGQRPLAVIHAKDEASWQEAAKAVKAAII 422
           VV +GGGR   SD +D +VG +++  LG  +     L ++HA DEA+   A   ++AA  
Sbjct: 360 VVQLGGGRMIESDVVDPAVGLSELTPLGQKLSVGDQLGIVHAADEAAADVAETRLRAAYQ 419

Query: 423 LDDKAPASTPSVYRRIT 439
           L D AP   P +Y+RI+
Sbjct: 420 LSDAAPDLPPLIYKRIS 436


Lambda     K      H
   0.319    0.134    0.377 

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: 506
Number of extensions: 23
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: 440
Length of database: 436
Length adjustment: 32
Effective length of query: 408
Effective length of database: 404
Effective search space:   164832
Effective search space used:   164832
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate GFF1179 PGA1_c11940 (thymidine phosphorylase DeoA)
to HMM TIGR02644 (pdp: pyrimidine-nucleoside phosphorylase (EC 2.4.2.2))

# 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/TIGR02644.hmm
# target sequence database:        /tmp/gapView.2681.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02644  [M=417]
Accession:   TIGR02644
Description: Y_phosphoryl: pyrimidine-nucleoside phosphorylase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   6.2e-140  452.6   2.4     7e-140  452.4   2.4    1.0  1  lcl|FitnessBrowser__Phaeo:GFF1179  PGA1_c11940 thymidine phosphoryl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF1179  PGA1_c11940 thymidine phosphorylase DeoA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  452.4   2.4    7e-140    7e-140       3     416 ..       5     420 ..       3     421 .. 0.97

  Alignments for each domain:
  == domain 1  score: 452.4 bits;  conditional E-value: 7e-140
                          TIGR02644   3 eiiekKrdgkklseeeinflingytkgeiadyQisallmaiyfkgldkeEtlalTkamvesGevldlselkkikvD 78 
                                         ii   r+g++ s+++++++ +g+++g+++d Q+ a++ma+ ++gl  e   alT am++sG+vl + +l++++ D
  lcl|FitnessBrowser__Phaeo:GFF1179   5 AIIASLRRGDTPSDADLRWFAEGLANGTVSDAQAGAFAMAVCLQGLGVEARGALTLAMRDSGDVLRW-DLDGPVLD 79 
                                        699999************************************************************9.69****** PP

                          TIGR02644  79 KHStGGvGDkvsLvlaPlvaalgvkvaklSGRgLghTGGTlDKLesipGfktelseeefieivkkvglaiigqtkd 154
                                        KHStGGvGD vsL+laP +a +g++v+++SGRgLghTGGTlDK+e+ipG+++++se++++++++ vg+ai+g+t++
  lcl|FitnessBrowser__Phaeo:GFF1179  80 KHSTGGVGDCVSLLLAPALAECGAYVPMISGRGLGHTGGTLDKMEAIPGVSIQVSEQDLVAMMQGVGCAIVGATAQ 155
                                        **************************************************************************** PP

                          TIGR02644 155 lapaDkklYalRdvtgTvdslpLiasSilsKKlaagadalvlDvkvGkGaFmktleeakeLakelveigkkagrkv 230
                                        +apaDk+lYa+Rdvt+Tvdsl Li++SilsKKlaa +dalvlDvk+G+GaFmktleea++La +l e +++ag ++
  lcl|FitnessBrowser__Phaeo:GFF1179 156 IAPADKRLYAIRDVTATVDSLDLITASILSKKLAASTDALVLDVKIGSGAFMKTLEEAEALALSLTETANAAGCRT 231
                                        **************************************************************************** PP

                          TIGR02644 231 valltdmnepLgkaiGNalEvkeavevLkge.gpa..dlkelvlalaaemlllaklakteeeakekleevlesgka 303
                                        +al+tdmn+pL+ a+GNalEv+e++ vL+g  g +   l+el+++ +  +l++ +la + e + e+++++++sg  
  lcl|FitnessBrowser__Phaeo:GFF1179 232 SALITDMNQPLAPALGNALEVAEVMRVLTGVsG-QggALTELTAEQGGVLLAHGGLAADAEAGAEMIRKAIASGAV 306
                                        ******************************963.446*************************************** PP

                          TIGR02644 304 lekfkefveaqgGdle.vlkeekklakakkkeevkaeksgvieeidaeelgliavelgaGRakkedkidleaGiel 378
                                        +e+f+++v+a gG  +  ++ ++ l++a  ++++k e+ g+++ id e+lgl++v+lg+GR+ ++d +d+++G++ 
  lcl|FitnessBrowser__Phaeo:GFF1179 307 AERFARMVAAMGGSSDfAETWQTILPTAPVQRRIKVEQTGYVSAIDGEALGLAVVQLGGGRMIESDVVDPAVGLSE 382
                                        ****************5555677789999*********************************************** PP

                          TIGR02644 379 ekkvgdkvkkgdllltlyssdeekaeeaakalkkaiki 416
                                         +  g+k+++gd+l  +++ de+ a+ a+++l++a+++
  lcl|FitnessBrowser__Phaeo:GFF1179 383 LTPLGQKLSVGDQLGIVHAADEAAADVAETRLRAAYQL 420
                                        ********************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (417 nodes)
Target sequences:                          1  (436 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: 00:00:00.01
# Mc/sec: 9.68
//
[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