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; EC 2.4.2.4; TdRPase (uncharacterized)
to candidate WP_090439786.1 BLS63_RS03375 thymidine phosphorylase

Query= curated2:Q21W90
         (522 letters)



>NCBI__GCF_900100495.1:WP_090439786.1
          Length = 524

 Score =  766 bits (1979), Expect = 0.0
 Identities = 388/512 (75%), Positives = 444/512 (86%)

Query: 11  ASKLVLRRVAIDTYRENVAYLHRDCAVYRAEGFQALSKVEVRANGRHILATLNVVDDPNI 70
           A+ L LRRV IDTYRENVAYLHRDCA+YRAEGFQAL+KVEV ANGR ILA+LNVVDD  I
Sbjct: 13  ATPLRLRRVGIDTYRENVAYLHRDCALYRAEGFQALAKVEVSANGRRILASLNVVDDGCI 72

Query: 71  VACNELGLSEDAFAQMAVIDGQPASVSQAEPPQSIGALRRKLAGERLGREDFLGIVRDIA 130
           V  +ELGLSEDAFAQ+ V +G PAS+SQAEPP SI AL RK+AGERL REDF  IVRDIA
Sbjct: 73  VGLDELGLSEDAFAQLGVDNGHPASISQAEPPGSIPALHRKIAGERLAREDFQAIVRDIA 132

Query: 131 ELHYSKIELSAFVVATNRDELDREEVYFLTEAMVASGRTLNWHEPLVVDKHCIGGIPGNR 190
           E  YSKIEL+AFVVA N+ ELDREEVYFL++AM   GR L+WHE  VVDKHCIGGIPGNR
Sbjct: 133 EHRYSKIELTAFVVACNQGELDREEVYFLSDAMARVGRQLDWHEHPVVDKHCIGGIPGNR 192

Query: 191 SSMLVVPIVAAHGLLCPKTSSRAITSPAGTADTMEVLAKVELPVDQLADIVRTHRGCLAW 250
           +SMLVVPIVAAHG+LCPKTSSRAITSPAGTADTMEVLA VELP ++L +IVR HRGCLAW
Sbjct: 193 TSMLVVPIVAAHGMLCPKTSSRAITSPAGTADTMEVLANVELPFERLEEIVREHRGCLAW 252

Query: 251 GGAAHLSPADDVLISVERPLAIDSPGQMVASILSKKIAAGSTHLVLDIPIGPSAKVRSMP 310
           GG + LSPADDVLI+VERPL+IDSPGQMVASILSKK+AAGSTHL+LDIP+GP+AKVRSMP
Sbjct: 253 GGTSELSPADDVLIAVERPLSIDSPGQMVASILSKKLAAGSTHLLLDIPVGPTAKVRSMP 312

Query: 311 EAQRLRRLFEYVAGRMHLSLDVVVTDGRQPIGNGIGPVLEARDVMRVLENDPRAPNDLRQ 370
           EAQRLR+LFEYVAGRM L +DVV++DGRQP+G GIGPVLEARDVM VL N+P APNDLRQ
Sbjct: 313 EAQRLRKLFEYVAGRMGLVIDVVISDGRQPVGRGIGPVLEARDVMAVLHNEPAAPNDLRQ 372

Query: 371 KSLRLAGRLIEFDPDVRGGDGFAIARDILDSGRALAKMNAIIAAQGAKPFDHNHPQLGAL 430
           K+LRLAGR++EFDPDVRGGDGFAIAR+ILDSGRALAKM AI+ AQGA+ FD   P L  L
Sbjct: 373 KALRLAGRVLEFDPDVRGGDGFAIAREILDSGRALAKMRAIMQAQGARAFDPQRPPLAPL 432

Query: 431 TFDICASESGVVTGIDNLQVARIARLAGAPKVIGAGIDLFHKLGEAVTSGEVLYRVHAGF 490
           +F+I A  S VV+ IDNLQ+ARIARLAGAPKV GAG++L  KLGE V +GE LYRV+A +
Sbjct: 433 SFEIGAERSAVVSAIDNLQLARIARLAGAPKVQGAGVELLRKLGEPVQAGEPLYRVYAAY 492

Query: 491 QSDLDFARQACAKSTGYTLGRAEDVPHVFTEF 522
            +DL+FARQAC + +G++LG A++V  +F EF
Sbjct: 493 PADLEFARQACTRHSGFSLGTADEVTPLFVEF 524


Lambda     K      H
   0.320    0.137    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: 929
Number of extensions: 30
Number of successful extensions: 1
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: 522
Length of database: 524
Length adjustment: 35
Effective length of query: 487
Effective length of database: 489
Effective search space:   238143
Effective search space used:   238143
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_090439786.1 BLS63_RS03375 (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.20636.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-185  603.5   0.0   1.5e-185  603.2   0.0    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090439786.1  BLS63_RS03375 thymidine phosphor


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090439786.1  BLS63_RS03375 thymidine phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  603.2   0.0  1.5e-185  1.5e-185       1     489 [.      16     509 ..      16     512 .. 0.98

  Alignments for each domain:
  == domain 1  score: 603.2 bits;  conditional E-value: 1.5e-185
                                 TIGR02645   1 lkvrvlnidtgqekvlinskd...lkeekltpqdrvevrlgkkslia..ivvssddlvesgevglseev 64 
                                               l++r+++idt +e+v + ++d    ++e++++ ++vev  +++ ++a  +vv+++ +v  +e+glse++
  lcl|NCBI__GCF_900100495.1:WP_090439786.1  16 LRLRRVGIDTYRENVAYLHRDcalYRAEGFQALAKVEVSANGRRILAslNVVDDGCIVGLDELGLSEDA 84 
                                               689******************88779*********************888899999************* PP

                                 TIGR02645  65 veeleekegdlvtvtpaekpeslrairkklrgkklkkeeikaivsdivdeklsdveisafltalaingl 133
                                               + +l + +g+  ++++ae+p s++a+++k+ g++l +e+ +aiv+di+++++s +e++af++a++ + l
  lcl|NCBI__GCF_900100495.1:WP_090439786.1  85 FAQLGVDNGHPASISQAEPPGSIPALHRKIAGERLAREDFQAIVRDIAEHRYSKIELTAFVVACNQGEL 153
                                               ********************************************************************* PP

                                 TIGR02645 134 dvdeiealtiamvetGetlewdrevivDkhsiGGvPGnktsllvvpivaaaGLliPktssraitsaaGt 202
                                               d +e+  l  am+  G +l+w+++++vDkh+iGG+PGn+ts+lvvpivaa+G+l Pktssraits+aGt
  lcl|NCBI__GCF_900100495.1:WP_090439786.1 154 DREEVYFLSDAMARVGRQLDWHEHPVVDKHCIGGIPGNRTSMLVVPIVAAHGMLCPKTSSRAITSPAGT 222
                                               ********************************************************************* PP

                                 TIGR02645 203 aDvvevltrvelsveelkrivekvggclvWGGalnlaPaDDvlikverpLslDpeeqllasilskkiai 271
                                               aD++evl++vel  e l +iv +  gcl+WGG  +l+PaDDvli verpLs+D+  q++asilskk+a+
  lcl|NCBI__GCF_900100495.1:WP_090439786.1 223 ADTMEVLANVELPFERLEEIVREHRGCLAWGGTSELSPADDVLIAVERPLSIDSPGQMVASILSKKLAA 291
                                               ********************************************************************* PP

                                 TIGR02645 272 GstkvliDiPvGpgakvksvkeaerLakdlielgkrlgvtvevvityGsqPiGraiGPaLeakealavL 340
                                               Gst++l+DiPvGp+akv+s+ ea+rL+k+++ ++ r+g +++vvi +G+qP+Gr+iGP+Lea++++avL
  lcl|NCBI__GCF_900100495.1:WP_090439786.1 292 GSTHLLLDIPVGPTAKVRSMPEAQRLRKLFEYVAGRMGLVIDVVISDGRQPVGRGIGPVLEARDVMAVL 360
                                               ********************************************************************* PP

                                 TIGR02645 341 esskeaPtsLvekslaLaaiLLemggaaergaGkelarelLdsGkaleklkeiieaqGgdniksediev 409
                                               +++++aP++L+ k+l+La+ +Le+++ ++ g G ++are+LdsG+al k++ i++aqG++  +++  ++
  lcl|NCBI__GCF_900100495.1:WP_090439786.1 361 HNEPAAPNDLRQKALRLAGRVLEFDPDVRGGDGFAIAREILDSGRALAKMRAIMQAQGARAFDPQRPPL 429
                                               ********************************************************************* PP

                                 TIGR02645 410 GklkadikaetdGyvteidnkaltriareaGaPedkgaGvklhvkvgdkvkkGdplytiyaeseekldk 478
                                                 l+++i ae++ +v++idn +l+riar+aGaP+ +gaGv+l +k+g+ v++G+ply++ya     l+ 
  lcl|NCBI__GCF_900100495.1:WP_090439786.1 430 APLSFEIGAERSAVVSAIDNLQLARIARLAGAPKVQGAGVELLRKLGEPVQAGEPLYRVYAAYPADLEF 498
                                               ****************************************************************99999 PP

                                 TIGR02645 479 aialaralepi 489
                                               a ++  +++++
  lcl|NCBI__GCF_900100495.1:WP_090439786.1 499 ARQACTRHSGF 509
                                               99888887765 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02
# Mc/sec: 12.31
//
[ok]

This GapMind analysis is from Sep 24 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