Alignments for a candidate for deoA in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Pseudomonas benzenivorans DSM 8628

Align Putative thymidine phosphorylase 1; EC 2.4.2.4; TdRPase 1 (uncharacterized)
to candidate WP_090447525.1 BLS63_RS19870 thymidine phosphorylase

Query= curated2:A1W631
         (511 letters)



>NCBI__GCF_900100495.1:WP_090447525.1
          Length = 505

 Score =  577 bits (1488), Expect = e-169
 Identities = 301/496 (60%), Positives = 359/496 (72%)

Query: 16  LRAWRTGIDTYQEPIVYMRSDCVVCRSEGFTTQTRVLLTAGTRSAVATLNVVEGNWLAPG 75
           LR  R GIDT+Q+ + +M  DC VCRSEGF+  +R+ L  G R  +ATL VV+G W+A G
Sbjct: 9   LRVRRLGIDTHQQAVAFMPRDCHVCRSEGFSALSRIELVKGARRVIATLMVVDGRWVAGG 68

Query: 76  VAGLSEAAWHALDPAADAWINVSYAPTLDSLSHVRAKVYGHRLDAGAFNAVIGDVAAGRY 135
             GLSE+AW  L       + V +   ++S+S VR K+YG  L   A  A++ D+ AGR+
Sbjct: 69  EVGLSESAWRLLGAQEGESVAVHHPAPVESMSAVRGKIYGSALSREALTAIVNDIDAGRF 128

Query: 136 SDLYLAAFVTACAGDRLDLSETVALTRAMVAVGHRLDWGRETVVDKHCVGGLPGNRTTLL 195
           SD+ LAAF+T CAG++L L+E   LT AMVAVG RL W R  V+DKHCVGGLPGNRTT +
Sbjct: 129 SDVELAAFLTGCAGNQLSLTEIGDLTEAMVAVGERLHWDRPLVLDKHCVGGLPGNRTTPI 188

Query: 196 VVPIVAACGLTMPKTSSRAITSPAGTADTMEVLAPVNLDIAAMRRTVERTGGCIVWGGSV 255
           VV IVAA GL MPKTSSRAITSPAGTAD ME LAPV LD+ AMRR VE+ GGC+VWGG+V
Sbjct: 189 VVAIVAANGLCMPKTSSRAITSPAGTADAMETLAPVALDLPAMRRVVEQEGGCVVWGGAV 248

Query: 256 RLSPADDVLIRVERPLDLDSEGQLVASVLSKKAAAGSTHVLIDLPVGPTAKVRSTEAAQS 315
           +LSP DDVLIRVER LDLDS+GQLVASVLSKK AAG++HVLID+PVG TAKVR   AA  
Sbjct: 249 QLSPTDDVLIRVERALDLDSQGQLVASVLSKKLAAGASHVLIDIPVGATAKVRDLPAAIQ 308

Query: 316 LGRRLVEVGRAIGLQVTLRITDGLQPVGRGVGPALEARDVLAVLRGQADAPDDLRQRALR 375
           L R LVEVG  +GL V + +++G  PVGRG+GPALEARDVLAVLRG A AP DLR+RAL 
Sbjct: 309 LQRLLVEVGSRLGLNVQVHVSNGDGPVGRGIGPALEARDVLAVLRGDAQAPQDLRERALD 368

Query: 376 LAGDILELGGAAPNGSGLQLAAEVLADGRAWAKFQAICEAQGGLREVPVTPYRQVITAAV 435
           LAG +LE+ G AP GSG  LA   LA G AW KFQAI  AQGGLRE P   YR  + A  
Sbjct: 369 LAGLLLEMSGQAPTGSGYALAEATLASGSAWRKFQAIANAQGGLREPPQARYRHPVLAGH 428

Query: 436 AGRVAAIDNRVLARAAKLAGAPKAPAAGVDVHARIGDPVQAGQPLFTLHAQTAGELDYAG 495
            GRV  IDNRVL+R  KLAGAP APAAG+ +   +G  V+A QPL+T+HA+T GEL YA 
Sbjct: 429 GGRVRRIDNRVLSRIGKLAGAPAAPAAGLVLGTALGQRVEADQPLYTVHAETPGELAYAL 488

Query: 496 HFVDTRPPIFQISEEA 511
            +    P +F I E+A
Sbjct: 489 EYAQQHPELFFIEEDA 504


Lambda     K      H
   0.319    0.134    0.396 

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: 723
Number of extensions: 33
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: 511
Length of database: 505
Length adjustment: 34
Effective length of query: 477
Effective length of database: 471
Effective search space:   224667
Effective search space used:   224667
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: 52 (24.6 bits)

Align candidate WP_090447525.1 BLS63_RS19870 (thymidine phosphorylase)
to HMM TIGR02645 (putative thymidine phosphorylase (EC 2.4.2.4))

# 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/TIGR02645.hmm
# target sequence database:        /tmp/gapView.22987.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02645  [M=493]
Accession:   TIGR02645
Description: ARCH_P_rylase: putative thymidine 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.2e-179  583.8   0.0   1.4e-179  583.5   0.0    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090447525.1  BLS63_RS19870 thymidine phosphor


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090447525.1  BLS63_RS19870 thymidine phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  583.5   0.0  1.4e-179  1.4e-179       1     487 [.       9     495 ..       9     500 .. 0.98

  Alignments for each domain:
  == domain 1  score: 583.5 bits;  conditional E-value: 1.4e-179
                                 TIGR02645   1 lkvrvlnidtgqekvlinskd...lkeekltpqdrvevrlgkkslia.ivvssddlvesgevglseevv 65 
                                               l+vr+l+idt+q+ v ++ +d   +++e++++ +r+e+  g + +ia ++v ++  v+ gevglse++ 
  lcl|NCBI__GCF_900100495.1:WP_090447525.1   9 LRVRRLGIDTHQQAVAFMPRDchvCRSEGFSALSRIELVKGARRVIAtLMVVDGRWVAGGEVGLSESAW 77 
                                               689******************9999*************99**9999976777889************** PP

                                 TIGR02645  66 eeleekegdlvtvtpaekpeslrairkklrgkklkkeeikaivsdivdeklsdveisafltalaingld 134
                                               + l ++eg+ v+v++  + es++a+r k++g+ l++e ++aiv+di   ++sdve++aflt++a n+l+
  lcl|NCBI__GCF_900100495.1:WP_090447525.1  78 RLLGAQEGESVAVHHPAPVESMSAVRGKIYGSALSREALTAIVNDIDAGRFSDVELAAFLTGCAGNQLS 146
                                               ********************************************************************* PP

                                 TIGR02645 135 vdeiealtiamvetGetlewdrevivDkhsiGGvPGnktsllvvpivaaaGLliPktssraitsaaGta 203
                                                 ei +lt+amv  Ge l+wdr+ ++Dkh++GG+PGn+t+++vv+ivaa+GL +Pktssraits+aGta
  lcl|NCBI__GCF_900100495.1:WP_090447525.1 147 LTEIGDLTEAMVAVGERLHWDRPLVLDKHCVGGLPGNRTTPIVVAIVAANGLCMPKTSSRAITSPAGTA 215
                                               ********************************************************************* PP

                                 TIGR02645 204 DvvevltrvelsveelkrivekvggclvWGGalnlaPaDDvlikverpLslDpeeqllasilskkiaiG 272
                                               D +e+l++v+l +  ++r+ve+ ggc+vWGGa++l+P DDvli+ver+L+lD++ ql+as+lskk+a+G
  lcl|NCBI__GCF_900100495.1:WP_090447525.1 216 DAMETLAPVALDLPAMRRVVEQEGGCVVWGGAVQLSPTDDVLIRVERALDLDSQGQLVASVLSKKLAAG 284
                                               ********************************************************************* PP

                                 TIGR02645 273 stkvliDiPvGpgakvksvkeaerLakdlielgkrlgvtvevvityGsqPiGraiGPaLeakealavLe 341
                                               +++vliDiPvG +akv+ +  a +L+++l+e+g+rlg +v+v + +G  P+Gr+iGPaLea+++lavL+
  lcl|NCBI__GCF_900100495.1:WP_090447525.1 285 ASHVLIDIPVGATAKVRDLPAAIQLQRLLVEVGSRLGLNVQVHVSNGDGPVGRGIGPALEARDVLAVLR 353
                                               ********************************************************************* PP

                                 TIGR02645 342 sskeaPtsLvekslaLaaiLLemggaaergaGkelarelLdsGkaleklkeiieaqGgdniksedievG 410
                                                + +aP++L+e++l La+ LLem+g+a++g+G++la+ +L+sG a++k++ i +aqGg    +e+ ++ 
  lcl|NCBI__GCF_900100495.1:WP_090447525.1 354 GDAQAPQDLRERALDLAGLLLEMSGQAPTGSGYALAEATLASGSAWRKFQAIANAQGGL---REPPQA- 418
                                               ***********************************************************...777777. PP

                                 TIGR02645 411 klkadikaetdGyvteidnkaltriareaGaPedkgaGvklhvkvgdkvkkGdplytiyaeseekldka 479
                                               +++  + a + G v +idn+ l ri ++aGaP    aG+ l   +g++v++ +plyt++ae+  +l +a
  lcl|NCBI__GCF_900100495.1:WP_090447525.1 419 RYRHPVLAGHGGRVRRIDNRVLSRIGKLAGAPAAPAAGLVLGTALGQRVEADQPLYTVHAETPGELAYA 487
                                               9******************************************************************** PP

                                 TIGR02645 480 ialarale 487
                                               +++a++++
  lcl|NCBI__GCF_900100495.1:WP_090447525.1 488 LEYAQQHP 495
                                               ****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (493 nodes)
Target sequences:                          1  (505 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: 00:00:00.03
# Mc/sec: 7.49
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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