Alignments for a candidate for deoA in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Dyella japonica UNC79MFTsu3.2

Align Putative thymidine phosphorylase 1; EC 2.4.2.4; TdRPase 1 (uncharacterized)
to candidate N515DRAFT_2462 N515DRAFT_2462 thymidine phosphorylase

Query= curated2:A1W631
         (511 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2462
          Length = 524

 Score =  539 bits (1388), Expect = e-157
 Identities = 282/491 (57%), Positives = 348/491 (70%), Gaps = 1/491 (0%)

Query: 20  RTGIDTYQEPIVYMRSDCVVCRSEGFTTQTRVLLTAGTRSAVATLNVVEGNWLAPGVAGL 79
           R GIDT  E ++Y+  D  +CR+EGF   +RV ++   R  +A LN+V G WLAP  AGL
Sbjct: 32  RVGIDTGDEHVIYLHEDSPICRAEGFGAHSRVQISIDERRLLARLNMVSGGWLAPEEAGL 91

Query: 80  SEAAWHALDPAADAWINVSYAPTLDSLSHVRAKVYGHRLDAGAFNAVIGDVAAGRYSDLY 139
           SE AW AL P        ++  +++SLS VRAK++G  L+   F A++ DVA  RYS L 
Sbjct: 92  SEPAWSALAPRLGETAMFAHPSSVESLSRVRAKIHGQPLNNEDFQAIMQDVAQRRYSALE 151

Query: 140 LAAFVTACAGDRLDLSETVALTRAMVAVGHRLDWGRETVVDKHCVGGLPGNRTTLLVVPI 199
           LAAFVTACA   L   E  +LT AMVA G RLDW R  V DKHC+GGLPGNRTT +VV I
Sbjct: 152 LAAFVTACANGHLTPREISSLTGAMVATGARLDWSRAIVADKHCIGGLPGNRTTPIVVAI 211

Query: 200 VAACGLTMPKTSSRAITSPAGTADTMEVLAPVNLDIAAMRRTVERTGGCIVWGGSVRLSP 259
             + GL MPKTSSRAITSPAGTADTME+LAPV+L +  MR  VERTGGC++WGGS+ LSP
Sbjct: 212 ATSLGLVMPKTSSRAITSPAGTADTMEMLAPVDLSLPRMREIVERTGGCLIWGGSIGLSP 271

Query: 260 ADDVLIRVERPLDLDSEGQLVASVLSKKAAAGSTHVLIDLPVGPTAKVRSTEAAQSLGRR 319
           ADDV+IR+ER LD+DSEGQLVASVLSKK AAGS+HVLID+PVGPTAK+R    A+SL   
Sbjct: 272 ADDVMIRIERALDIDSEGQLVASVLSKKIAAGSSHVLIDMPVGPTAKIRDMIEARSLAAC 331

Query: 320 LVEVGRAIGLQVTLRITDGLQPVGRGVGPALEARDVLAVLRGQADAPDDLRQRALRLAGD 379
           L +V R  G+ +    TDG QP+GRGVGPALEA DVLAVL+G+  AP DLR+RA+ LA  
Sbjct: 332 LQQVARDFGMHMRCVFTDGSQPIGRGVGPALEAHDVLAVLQGRPGAPLDLRERAIALASA 391

Query: 380 ILEL-GGAAPNGSGLQLAAEVLADGRAWAKFQAICEAQGGLREVPVTPYRQVITAAVAGR 438
           +LEL G AA      ++A E L  G AW +FQAICEAQGG+R       +  + +A+ GR
Sbjct: 392 LLELTGAAAGEVLATRMATEALDRGAAWRQFQAICEAQGGMRTPGRAAQQYPVRSALGGR 451

Query: 439 VAAIDNRVLARAAKLAGAPKAPAAGVDVHARIGDPVQAGQPLFTLHAQTAGELDYAGHFV 498
           V AIDNR L+R AKLAGAP +P AG+++H R+GD V+ GQP+FT+HAQT GEL YA  +V
Sbjct: 452 VHAIDNRQLSRTAKLAGAPMSPLAGLELHVRVGDRVEPGQPIFTVHAQTRGELAYAMEYV 511

Query: 499 DTRPPIFQISE 509
              P I  ++E
Sbjct: 512 RRHPCIVTLAE 522


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: 721
Number of extensions: 19
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: 511
Length of database: 524
Length adjustment: 35
Effective length of query: 476
Effective length of database: 489
Effective search space:   232764
Effective search space used:   232764
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 N515DRAFT_2462 N515DRAFT_2462 (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.13994.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   5.3e-179  581.6   0.0   6.4e-179  581.4   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_2462  N515DRAFT_2462 thymidine phospho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2462  N515DRAFT_2462 thymidine phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  581.4   0.0  6.4e-179  6.4e-179       2     489 ..      29     517 ..      28     520 .. 0.97

  Alignments for each domain:
  == domain 1  score: 581.4 bits;  conditional E-value: 6.4e-179
                                    TIGR02645   2 kvrvlnidtgqekvlinskd...lkeekltpqdrvevrlgkkslia..ivvssddlvesgevglse 62 
                                                  ++r+++idtg e+v++ ++d   +++e++ +++rv++ ++++ l+a  ++vs +  ++  e glse
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2462  29 QLRRVGIDTGDEHVIYLHEDspiCRAEGFGAHSRVQISIDERRLLArlNMVS-GGWLAPEEAGLSE 93 
                                                  689*******************************************644444.569999******* PP

                                    TIGR02645  63 evveeleekegdlvtvtpaekpeslrairkklrgkklkkeeikaivsdivdeklsdveisafltal 128
                                                  ++ ++l+ + g+     + ++ esl+ +r+k++g++l++e+ +ai++d++++++s +e++af+ta+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2462  94 PAWSALAPRLGETAMFAHPSSVESLSRVRAKIHGQPLNNEDFQAIMQDVAQRRYSALELAAFVTAC 159
                                                  ****************************************************************** PP

                                    TIGR02645 129 aingldvdeiealtiamvetGetlewdrevivDkhsiGGvPGnktsllvvpivaaaGLliPktssr 194
                                                  a + l+  ei  lt amv tG  l+w r +++Dkh+iGG+PGn+t+++vv+i+ + GL +Pktssr
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2462 160 ANGHLTPREISSLTGAMVATGARLDWSRAIVADKHCIGGLPGNRTTPIVVAIATSLGLVMPKTSSR 225
                                                  ****************************************************************** PP

                                    TIGR02645 195 aitsaaGtaDvvevltrvelsveelkrivekvggclvWGGalnlaPaDDvlikverpLslDpeeql 260
                                                  aits+aGtaD++e+l++v+ls+  +++ive++ggcl+WGG + l+PaDDv+i++er+L++D+e ql
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2462 226 AITSPAGTADTMEMLAPVDLSLPRMREIVERTGGCLIWGGSIGLSPADDVMIRIERALDIDSEGQL 291
                                                  ****************************************************************** PP

                                    TIGR02645 261 lasilskkiaiGstkvliDiPvGpgakvksvkeaerLakdlielgkrlgvtvevvityGsqPiGra 326
                                                  +as+lskkia+Gs++vliD+PvGp+ak++ + ea++La  l+++++ +g+++ +v t+GsqPiGr+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2462 292 VASVLSKKIAAGSSHVLIDMPVGPTAKIRDMIEARSLAACLQQVARDFGMHMRCVFTDGSQPIGRG 357
                                                  ****************************************************************** PP

                                    TIGR02645 327 iGPaLeakealavLesskeaPtsLvekslaLaaiLLemggaaerga.GkelarelLdsGkaleklk 391
                                                  +GPaLea+++lavL+  + aP +L+e+++aLa+ LLe++gaa  +    ++a+e Ld+G+a+++++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2462 358 VGPALEAHDVLAVLQGRPGAPLDLRERAIALASALLELTGAAAGEVlATRMATEALDRGAAWRQFQ 423
                                                  ****************************************9987753789**************** PP

                                    TIGR02645 392 eiieaqGgdniksedievGklkadikaetdGyvteidnkaltriareaGaPedkgaGvklhvkvgd 457
                                                   i+eaqGg    ++++ +   ++ + ++  G v +idn++l r a++aGaP+   aG++lhv+vgd
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2462 424 AICEAQGGM---RTPGRA-AQQYPVRSALGGRVHAIDNRQLSRTAKLAGAPMSPLAGLELHVRVGD 485
                                                  *********...888888.7899******************************************* PP

                                    TIGR02645 458 kvkkGdplytiyaeseekldkaialaralepi 489
                                                  +v+ G+p++t++a++  +l +a+++ r+++ i
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2462 486 RVEPGQPIFTVHAQTRGELAYAMEYVRRHPCI 517
                                                  ***************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (493 nodes)
Target sequences:                          1  (524 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 7.37
//
[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