Alignments for a candidate for deoA in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for deoA in Halomonas desiderata SP1

Align Putative thymidine phosphorylase; EC 2.4.2.4; TdRPase (uncharacterized)
to candidate WP_086510737.1 BZY95_RS15125 thymidine phosphorylase

Query= curated2:Q21W90
         (522 letters)



>NCBI__GCF_002151265.1:WP_086510737.1
          Length = 530

 Score =  733 bits (1893), Expect = 0.0
 Identities = 371/509 (72%), Positives = 430/509 (84%)

Query: 14  LVLRRVAIDTYRENVAYLHRDCAVYRAEGFQALSKVEVRANGRHILATLNVVDDPNIVAC 73
           L L RVAIDTYRENVAYLHR+C +YRAEGFQALSKVEVRANG+ ILATLNVVDD  IV  
Sbjct: 22  LALCRVAIDTYRENVAYLHRECDLYRAEGFQALSKVEVRANGKRILATLNVVDDVAIVGH 81

Query: 74  NELGLSEDAFAQMAVIDGQPASVSQAEPPQSIGALRRKLAGERLGREDFLGIVRDIAELH 133
            +LGLSEDAFA + V +G P SVSQAEPP SI ALRRK+AGERL R+DF  IV+DIAEL 
Sbjct: 82  TQLGLSEDAFALLGVAEGHPVSVSQAEPPASIPALRRKIAGERLSRQDFREIVQDIAELR 141

Query: 134 YSKIELSAFVVATNRDELDREEVYFLTEAMVASGRTLNWHEPLVVDKHCIGGIPGNRSSM 193
           YSKIEL+AFVVA    ELDREEV++L++AM   GR L+WHE  VVDKHCIGGIPGNR+SM
Sbjct: 142 YSKIELTAFVVACELGELDREEVFYLSDAMGRVGRRLDWHEHPVVDKHCIGGIPGNRTSM 201

Query: 194 LVVPIVAAHGLLCPKTSSRAITSPAGTADTMEVLAKVELPVDQLADIVRTHRGCLAWGGA 253
           LVVPIVAAHGLLCPKTSSRAITSP+GTADTMEVLAKVE+P D+L ++VRTHRGC+AWGG 
Sbjct: 202 LVVPIVAAHGLLCPKTSSRAITSPSGTADTMEVLAKVEVPFDELGELVRTHRGCVAWGGT 261

Query: 254 AHLSPADDVLISVERPLAIDSPGQMVASILSKKIAAGSTHLVLDIPIGPSAKVRSMPEAQ 313
           + LSPADDVLI+VERPL+IDSPGQMVASILSKKIAAGSTHL+LDIP+GP AKVRSMPEA+
Sbjct: 262 SELSPADDVLIAVERPLSIDSPGQMVASILSKKIAAGSTHLLLDIPVGPHAKVRSMPEAR 321

Query: 314 RLRRLFEYVAGRMHLSLDVVVTDGRQPIGNGIGPVLEARDVMRVLENDPRAPNDLRQKSL 373
           RLR+LFE+VAGRM L LDVV+TDG QPIG GIGPVLEARDVMRVL N P AP DLRQKSL
Sbjct: 322 RLRKLFEFVAGRMGLVLDVVITDGSQPIGRGIGPVLEARDVMRVLTNHPDAPMDLRQKSL 381

Query: 374 RLAGRLIEFDPDVRGGDGFAIARDILDSGRALAKMNAIIAAQGAKPFDHNHPQLGALTFD 433
           RLAGR++EFDPD+RGGDGF IARDILDSGRAL KM AII AQG KPFD + P+L    F+
Sbjct: 382 RLAGRMLEFDPDIRGGDGFGIARDILDSGRALEKMQAIIRAQGEKPFDLDDPELAPHRFE 441

Query: 434 ICASESGVVTGIDNLQVARIARLAGAPKVIGAGIDLFHKLGEAVTSGEVLYRVHAGFQSD 493
           + A ++GVVT IDNL++ARIARLAGAPK  GAG+DL  ++G+ V  G+ LYRVHA ++S+
Sbjct: 442 VLAPQAGVVTAIDNLRLARIARLAGAPKARGAGVDLLARIGDRVEQGQPLYRVHAAYRSE 501

Query: 494 LDFARQACAKSTGYTLGRAEDVPHVFTEF 522
             FA Q   + +G+ +G+ +++  +  EF
Sbjct: 502 HGFALQCSERDSGFDIGQPDEIQRLNVEF 530


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: 944
Number of extensions: 38
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: 530
Length adjustment: 35
Effective length of query: 487
Effective length of database: 495
Effective search space:   241065
Effective search space used:   241065
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_086510737.1 BZY95_RS15125 (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.2718.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-187  609.2   0.0   2.6e-187  609.0   0.0    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086510737.1  BZY95_RS15125 thymidine phosphor


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086510737.1  BZY95_RS15125 thymidine phosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  609.0   0.0  2.6e-187  2.6e-187       3     489 ..      24     515 ..      22     519 .. 0.98

  Alignments for each domain:
  == domain 1  score: 609.0 bits;  conditional E-value: 2.6e-187
                                 TIGR02645   3 vrvlnidtgqekvlinskd...lkeekltpqdrvevrlgkkslia..ivvssddlvesgevglseevve 66 
                                               + ++ idt +e+v + +++    ++e++++ ++vevr ++k ++a  +vv++  +v ++++glse+++ 
  lcl|NCBI__GCF_002151265.1:WP_086510737.1  24 LCRVAIDTYRENVAYLHREcdlYRAEGFQALSKVEVRANGKRILAtlNVVDDVAIVGHTQLGLSEDAFA 92 
                                               56789*************97777**********************77788888899************* PP

                                 TIGR02645  67 eleekegdlvtvtpaekpeslrairkklrgkklkkeeikaivsdivdeklsdveisafltalaingldv 135
                                                l + eg+ v+v++ae+p s++a+r+k+ g++l++++  +iv+di++ ++s +e++af++a++ + ld 
  lcl|NCBI__GCF_002151265.1:WP_086510737.1  93 LLGVAEGHPVSVSQAEPPASIPALRRKIAGERLSRQDFREIVQDIAELRYSKIELTAFVVACELGELDR 161
                                               ********************************************************************* PP

                                 TIGR02645 136 deiealtiamvetGetlewdrevivDkhsiGGvPGnktsllvvpivaaaGLliPktssraitsaaGtaD 204
                                               +e+  l  am   G  l+w+++++vDkh+iGG+PGn+ts+lvvpivaa+GLl Pktssraits++GtaD
  lcl|NCBI__GCF_002151265.1:WP_086510737.1 162 EEVFYLSDAMGRVGRRLDWHEHPVVDKHCIGGIPGNRTSMLVVPIVAAHGLLCPKTSSRAITSPSGTAD 230
                                               ********************************************************************* PP

                                 TIGR02645 205 vvevltrvelsveelkrivekvggclvWGGalnlaPaDDvlikverpLslDpeeqllasilskkiaiGs 273
                                               ++evl++ve+  +el ++v    gc++WGG  +l+PaDDvli verpLs+D+  q++asilskkia+Gs
  lcl|NCBI__GCF_002151265.1:WP_086510737.1 231 TMEVLAKVEVPFDELGELVRTHRGCVAWGGTSELSPADDVLIAVERPLSIDSPGQMVASILSKKIAAGS 299
                                               ********************************************************************* PP

                                 TIGR02645 274 tkvliDiPvGpgakvksvkeaerLakdlielgkrlgvtvevvityGsqPiGraiGPaLeakealavLes 342
                                               t++l+DiPvGp akv+s+ ea+rL+k++++++ r+g + +vvit+GsqPiGr+iGP+Lea+++++vL++
  lcl|NCBI__GCF_002151265.1:WP_086510737.1 300 THLLLDIPVGPHAKVRSMPEARRLRKLFEFVAGRMGLVLDVVITDGSQPIGRGIGPVLEARDVMRVLTN 368
                                               ********************************************************************* PP

                                 TIGR02645 343 skeaPtsLvekslaLaaiLLemggaaergaGkelarelLdsGkaleklkeiieaqGgdniksedievGk 411
                                               +++aP++L+ ksl+La+ +Le+++ ++ g G  +ar++LdsG+alek++ ii aqG +  + +d e+  
  lcl|NCBI__GCF_002151265.1:WP_086510737.1 369 HPDAPMDLRQKSLRLAGRMLEFDPDIRGGDGFGIARDILDSGRALEKMQAIIRAQGEKPFDLDDPELAP 437
                                               ********************************************************************* PP

                                 TIGR02645 412 lkadikaetdGyvteidnkaltriareaGaPedkgaGvklhvkvgdkvkkGdplytiyaeseekldkai 480
                                                ++++ a++ G+vt+idn +l+riar+aGaP+ +gaGv l  ++gd+v++G+ply+++a   +++  a+
  lcl|NCBI__GCF_002151265.1:WP_086510737.1 438 HRFEVLAPQAGVVTAIDNLRLARIARLAGAPKARGAGVDLLARIGDRVEQGQPLYRVHAAYRSEHGFAL 506
                                               ********************************************************************9 PP

                                 TIGR02645 481 alaralepi 489
                                               + +++ +++
  lcl|NCBI__GCF_002151265.1:WP_086510737.1 507 QCSERDSGF 515
                                               998887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (493 nodes)
Target sequences:                          1  (530 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 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 13.06
//
[ok]

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

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

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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