Alignments for a candidate for deoA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Cupriavidus basilensis 4G11

Align Putative thymidine phosphorylase 1; EC 2.4.2.4; TdRPase 1 (uncharacterized)
to candidate RR42_RS11670 RR42_RS11670 thymidine phosphorylase

Query= curated2:Q0KA59
         (520 letters)



>FitnessBrowser__Cup4G11:RR42_RS11670
          Length = 510

 Score =  660 bits (1702), Expect = 0.0
 Identities = 338/493 (68%), Positives = 402/493 (81%), Gaps = 2/493 (0%)

Query: 29  LVFRPLEIDTWQEHVIYMHPDCPVCRAEGFSAQARVRVQIGD--RSLIATLTLLGAPLLN 86
           L F+PLEIDT+QEHVIYMH DC VC AEGFSAQ RV+V  G   +SLIATL ++G  LL 
Sbjct: 12  LTFKPLEIDTYQEHVIYMHRDCVVCHAEGFSAQTRVQVSTGAGAQSLIATLNVVGDALLA 71

Query: 87  TGEASLSLSAARTLSARAGDVVHVTHAPALESVRALRAKIYGCHLDSVQLDGIIGDISAG 146
             +  LS  A++ L   AGD++ VTHAP LES+RA+R+KI+G  LD+ QL  I+GDISAG
Sbjct: 72  PSQVGLSSGASQQLGVAAGDIIAVTHAPGLESLRAVRSKIHGNPLDAPQLCAIMGDISAG 131

Query: 147 RYADVHIAAFLTACADGRMSLRETVDLTRAMVRSGQRLNWDREVVADKHCVGGLPGNRTT 206
           RY+DVHIAAFL+ACA GRM+ +ETVDLT AM+ +G RL+WDR VVADKHCVGGLPGNRT+
Sbjct: 132 RYSDVHIAAFLSACAGGRMTTQETVDLTCAMLDTGDRLDWDRPVVADKHCVGGLPGNRTS 191

Query: 207 PVVVAIAAAAGLLLPKTSSRAITSPAGTADTMEALTRVTLDSTELRRVVEQVGAALVWGG 266
           P+VVAI AAAGLLLPKTSSRAITSPAGTADTME LTRVTL + E+RRVVE+VGAALVWGG
Sbjct: 192 PIVVAICAAAGLLLPKTSSRAITSPAGTADTMEVLTRVTLSAAEMRRVVERVGAALVWGG 251

Query: 267 ALSLSPADDVLIRVERALDIDSDAQLVASILSKKIAAGSTHVLIDVPVGPTAKIREDSDL 326
           +L+LSPADDVLIRVERAL+IDSDAQLVAS+LSKK+AAGSTHVLIDVP+GPTAK+R D+DL
Sbjct: 252 SLTLSPADDVLIRVERALEIDSDAQLVASVLSKKLAAGSTHVLIDVPLGPTAKVRTDADL 311

Query: 327 ARLDLAMTKVADAFGLKLRILRTDGSQPVGRGVGPALEALDVLAVLQCQPTAPADLRERS 386
           ARL L + +VA AFG+ + ++ TDGSQPVGRG+GPALEA DVLAVLQ   +APADLR R+
Sbjct: 312 ARLRLLLEEVARAFGMHVLVVHTDGSQPVGRGIGPALEARDVLAVLQGAESAPADLRGRA 371

Query: 387 LLLAGELLEFCGAIPPGQGRLLAGSLLDSGAAWARFQAICEAQGGLRTPGQAVFRRDVVA 446
           LLL+  L+EFCGA+P GQG  LA  LL  GAAWA+FQAICEAQGGLR PG A  RR+++A
Sbjct: 372 LLLSASLMEFCGAVPAGQGLALATRLLADGAAWAKFQAICEAQGGLRQPGSAPLRREILA 431

Query: 447 ARSGIVTSVDNRHVARTAKLAGAPRRQVAGLELHVRAGDEVVAGAPLCTLHAQASGELEY 506
              GIVTS+DNR ++R AKLAGAP R+ AG+++HVR  D V AG PL T+HA A GEL Y
Sbjct: 432 PADGIVTSIDNRLLSRAAKLAGAPNRKAAGIDMHVRLNDAVRAGQPLFTIHALAQGELAY 491

Query: 507 AFSYALAHDPFRI 519
           + ++   H    I
Sbjct: 492 SQNFLTTHPAINI 504


Lambda     K      H
   0.320    0.135    0.391 

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: 848
Number of extensions: 27
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: 520
Length of database: 510
Length adjustment: 35
Effective length of query: 485
Effective length of database: 475
Effective search space:   230375
Effective search space used:   230375
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 RR42_RS11670 RR42_RS11670 (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.2636.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.4e-197  642.9   0.4   1.6e-197  642.7   0.4    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS11670  RR42_RS11670 thymidine phosphory


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS11670  RR42_RS11670 thymidine phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  642.7   0.4  1.6e-197  1.6e-197       1     491 [.      12     504 ..      12     506 .. 0.97

  Alignments for each domain:
  == domain 1  score: 642.7 bits;  conditional E-value: 1.6e-197
                                 TIGR02645   1 lkvrvlnidtgqekvlinskd...lkeekltpqdrvevrl..gkkslia..ivvssddlvesgevglse 62 
                                               l++++l+idt qe+v+++++d   +++e++++q rv+v    g +slia  +v  +d l++ ++vgls 
  lcl|FitnessBrowser__Cup4G11:RR42_RS11670  12 LTFKPLEIDTYQEHVIYMHRDcvvCHAEGFSAQTRVQVSTgaGAQSLIAtlNV-VGDALLAPSQVGLSS 79 
                                               689******************9999*************9722579****5333.4567*********** PP

                                 TIGR02645  63 evveeleekegdlvtvtpaekpeslrairkklrgkklkkeeikaivsdivdeklsdveisafltalain 131
                                                + ++l +  gd+++vt+a+ +eslra+r k++g++l+  ++ ai+ di   ++sdv+i+afl+a+a +
  lcl|FitnessBrowser__Cup4G11:RR42_RS11670  80 GASQQLGVAAGDIIAVTHAPGLESLRAVRSKIHGNPLDAPQLCAIMGDISAGRYSDVHIAAFLSACAGG 148
                                               ********************************************************************* PP

                                 TIGR02645 132 gldvdeiealtiamvetGetlewdrevivDkhsiGGvPGnktsllvvpivaaaGLliPktssraitsaa 200
                                               +++++e+++lt am +tG+ l+wdr+v++Dkh++GG+PGn+ts++vv+i aaaGLl+Pktssraits+a
  lcl|FitnessBrowser__Cup4G11:RR42_RS11670 149 RMTTQETVDLTCAMLDTGDRLDWDRPVVADKHCVGGLPGNRTSPIVVAICAAAGLLLPKTSSRAITSPA 217
                                               ********************************************************************* PP

                                 TIGR02645 201 GtaDvvevltrvelsveelkrivekvggclvWGGalnlaPaDDvlikverpLslDpeeqllasilskki 269
                                               GtaD++evltrv+ls+ e++r+ve+vg++lvWGG l l+PaDDvli+ver+L++D+++ql+as+lskk+
  lcl|FitnessBrowser__Cup4G11:RR42_RS11670 218 GTADTMEVLTRVTLSAAEMRRVVERVGAALVWGGSLTLSPADDVLIRVERALEIDSDAQLVASVLSKKL 286
                                               ********************************************************************* PP

                                 TIGR02645 270 aiGstkvliDiPvGpgakvksvkeaerLakdlielgkrlgvtvevvityGsqPiGraiGPaLeakeala 338
                                               a+Gst+vliD+P Gp+akv++  ++ rL+ +l+e+++ +g++v vv t+GsqP+Gr+iGPaLea+++la
  lcl|FitnessBrowser__Cup4G11:RR42_RS11670 287 AAGSTHVLIDVPLGPTAKVRTDADLARLRLLLEEVARAFGMHVLVVHTDGSQPVGRGIGPALEARDVLA 355
                                               ********************************************************************* PP

                                 TIGR02645 339 vLesskeaPtsLvekslaLaaiLLemggaaergaGkelarelLdsGkaleklkeiieaqGgdniksedi 407
                                               vL+  ++aP +L+ ++l L+a L+e++ga++ g+G +la+ lL+ G+a+ k++ i+eaqGg    ++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS11670 356 VLQGAESAPADLRGRALLLSASLMEFCGAVPAGQGLALATRLLADGAAWAKFQAICEAQGGL---RQPG 421
                                               **************************************************************...8888 PP

                                 TIGR02645 408 evGklkadikaetdGyvteidnkaltriareaGaPedkgaGvklhvkvgdkvkkGdplytiyaeseekl 476
                                                +  l+++i a+ dG+vt+idn+ l r a++aGaP++k aG+ +hv+++d v++G+pl+ti+a ++ +l
  lcl|FitnessBrowser__Cup4G11:RR42_RS11670 422 SA-PLRREILAPADGIVTSIDNRLLSRAAKLAGAPNRKAAGIDMHVRLNDAVRAGQPLFTIHALAQGEL 489
                                               87.89**************************************************************** PP

                                 TIGR02645 477 dkaialaralepikv 491
                                                ++ +   ++++i++
  lcl|FitnessBrowser__Cup4G11:RR42_RS11670 490 AYSQNFLTTHPAINI 504
                                               **9999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (493 nodes)
Target sequences:                          1  (510 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: 00:00:00.02
# Mc/sec: 9.39
//
[ok]

This GapMind analysis is from Sep 17 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