GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoA in Acidovorax caeni R-24608

Align Putative thymidine phosphorylase; EC 2.4.2.4; TdRPase (uncharacterized)
to candidate WP_082366649.1 BN2503_RS16620 thymidine phosphorylase family protein

Query= curated2:Q21W90
         (522 letters)



>NCBI__GCF_001298675.1:WP_082366649.1
          Length = 531

 Score =  823 bits (2125), Expect = 0.0
 Identities = 418/511 (81%), Positives = 458/511 (89%)

Query: 12  SKLVLRRVAIDTYRENVAYLHRDCAVYRAEGFQALSKVEVRANGRHILATLNVVDDPNIV 71
           S+L +RRVAIDT+RENVAYLHRDCAVYRAEGFQALSK+EVRANGR ILATLNVVDD  IV
Sbjct: 21  SRLAVRRVAIDTWRENVAYLHRDCAVYRAEGFQALSKIEVRANGRRILATLNVVDDLGIV 80

Query: 72  ACNELGLSEDAFAQMAVIDGQPASVSQAEPPQSIGALRRKLAGERLGREDFLGIVRDIAE 131
           AC+ELGLSEDAFA + V  G   +V+QAEPP+S+GAL RK+AGERL RED   IVRDIAE
Sbjct: 81  ACDELGLSEDAFALLGVEAGYKVAVAQAEPPESMGALFRKIAGERLQREDLRAIVRDIAE 140

Query: 132 LHYSKIELSAFVVATNRDELDREEVYFLTEAMVASGRTLNWHEPLVVDKHCIGGIPGNRS 191
             YSKIEL+AFVVA NRDELDREEV+FL++AMVA+G+ L+WHE LVVDKHCIGGIPGNR+
Sbjct: 141 HRYSKIELTAFVVACNRDELDREEVFFLSDAMVATGQRLDWHEGLVVDKHCIGGIPGNRT 200

Query: 192 SMLVVPIVAAHGLLCPKTSSRAITSPAGTADTMEVLAKVELPVDQLADIVRTHRGCLAWG 251
           SMLVVPIVAAHG+LCPKTSSRAITSPAGTADTMEVLA VELP+  L  IVR HRGCLAWG
Sbjct: 201 SMLVVPIVAAHGMLCPKTSSRAITSPAGTADTMEVLANVELPLQDLQRIVRDHRGCLAWG 260

Query: 252 GAAHLSPADDVLISVERPLAIDSPGQMVASILSKKIAAGSTHLVLDIPIGPSAKVRSMPE 311
           G A LSPADDVLISVERPL+IDSPGQMVASILSKKIAAGSTHLVLDIPIGP+AKVRSMPE
Sbjct: 261 GTAQLSPADDVLISVERPLSIDSPGQMVASILSKKIAAGSTHLVLDIPIGPTAKVRSMPE 320

Query: 312 AQRLRRLFEYVAGRMHLSLDVVVTDGRQPIGNGIGPVLEARDVMRVLENDPRAPNDLRQK 371
           AQRLRRLFEYVA R+ LSLDVV+TDGRQPIGNGIGPVLEARDVMRVLENDPRAPNDLRQK
Sbjct: 321 AQRLRRLFEYVAQRLGLSLDVVITDGRQPIGNGIGPVLEARDVMRVLENDPRAPNDLRQK 380

Query: 372 SLRLAGRLIEFDPDVRGGDGFAIARDILDSGRALAKMNAIIAAQGAKPFDHNHPQLGALT 431
           SLRLAGRLIE DPDVRGGDG+AIARDILDSGRALA+M AIIAAQG K FDHNHP+LGAL 
Sbjct: 381 SLRLAGRLIECDPDVRGGDGYAIARDILDSGRALARMQAIIAAQGGKAFDHNHPRLGALH 440

Query: 432 FDICASESGVVTGIDNLQVARIARLAGAPKVIGAGIDLFHKLGEAVTSGEVLYRVHAGFQ 491
           F++CA   GVV GIDN Q+ARIARLAGAPKV GAG+DL  KLG+AV SG+ LYRVHA F 
Sbjct: 441 FEVCAPADGVVAGIDNQQIARIARLAGAPKVQGAGVDLLCKLGDAVVSGQPLYRVHADFS 500

Query: 492 SDLDFARQACAKSTGYTLGRAEDVPHVFTEF 522
           +DL+FARQACA+ +GY LG A++VP VF EF
Sbjct: 501 ADLEFARQACAQGSGYRLGTADEVPRVFVEF 531


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: 957
Number of extensions: 32
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: 531
Length adjustment: 35
Effective length of query: 487
Effective length of database: 496
Effective search space:   241552
Effective search space used:   241552
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_082366649.1 BN2503_RS16620 (thymidine phosphorylase family protein)
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.4043251.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   8.7e-192  623.8   0.0   1.1e-191  623.5   0.0    1.0  1  NCBI__GCF_001298675.1:WP_082366649.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001298675.1:WP_082366649.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  623.5   0.0  1.1e-191  1.1e-191       1     487 [.      23     514 ..      23     519 .. 0.98

  Alignments for each domain:
  == domain 1  score: 623.5 bits;  conditional E-value: 1.1e-191
                             TIGR02645   1 lkvrvlnidtgqekvlinskd...lkeekltpqdrvevrlgkkslia..ivvssddlvesgevglseevveel 68 
                                           l vr++ idt++e+v + ++d    ++e++++ +++evr +++ ++a  +vv++  +v+ +e+glse+++  l
  NCBI__GCF_001298675.1:WP_082366649.1  23 LAVRRVAIDTWRENVAYLHRDcavYRAEGFQALSKIEVRANGRRILAtlNVVDDLGIVACDELGLSEDAFALL 95 
                                           579******************87779*********************6666666678**************** PP

                             TIGR02645  69 eekegdlvtvtpaekpeslrairkklrgkklkkeeikaivsdivdeklsdveisafltalaingldvdeieal 141
                                            ++ g  v+v +ae+pes+ a+ +k+ g++l++e++ aiv+di+++++s +e++af++a++ + ld +e+  l
  NCBI__GCF_001298675.1:WP_082366649.1  96 GVEAGYKVAVAQAEPPESMGALFRKIAGERLQREDLRAIVRDIAEHRYSKIELTAFVVACNRDELDREEVFFL 168
                                           ************************************************************************* PP

                             TIGR02645 142 tiamvetGetlewdrevivDkhsiGGvPGnktsllvvpivaaaGLliPktssraitsaaGtaDvvevltrvel 214
                                             amv tG+ l+w++  +vDkh+iGG+PGn+ts+lvvpivaa+G+l Pktssraits+aGtaD++evl++vel
  NCBI__GCF_001298675.1:WP_082366649.1 169 SDAMVATGQRLDWHEGLVVDKHCIGGIPGNRTSMLVVPIVAAHGMLCPKTSSRAITSPAGTADTMEVLANVEL 241
                                           ************************************************************************* PP

                             TIGR02645 215 sveelkrivekvggclvWGGalnlaPaDDvlikverpLslDpeeqllasilskkiaiGstkvliDiPvGpgak 287
                                            +++l+riv    gcl+WGG  +l+PaDDvli+verpLs+D+  q++asilskkia+Gst++++DiP+Gp+ak
  NCBI__GCF_001298675.1:WP_082366649.1 242 PLQDLQRIVRDHRGCLAWGGTAQLSPADDVLISVERPLSIDSPGQMVASILSKKIAAGSTHLVLDIPIGPTAK 314
                                           ************************************************************************* PP

                             TIGR02645 288 vksvkeaerLakdlielgkrlgvtvevvityGsqPiGraiGPaLeakealavLesskeaPtsLvekslaLaai 360
                                           v+s+ ea+rL+++++ +++rlg   +vvit+G+qPiG++iGP+Lea+++++vLe++++aP++L+ ksl+La+ 
  NCBI__GCF_001298675.1:WP_082366649.1 315 VRSMPEAQRLRRLFEYVAQRLGLSLDVVITDGRQPIGNGIGPVLEARDVMRVLENDPRAPNDLRQKSLRLAGR 387
                                           ************************************************************************* PP

                             TIGR02645 361 LLemggaaergaGkelarelLdsGkaleklkeiieaqGgdniksedievGklkadikaetdGyvteidnkalt 433
                                           L+e ++ ++ g G+++ar++LdsG+al +++ ii aqGg+  ++++  +G l++++ a+ dG+v+ idn++++
  NCBI__GCF_001298675.1:WP_082366649.1 388 LIECDPDVRGGDGYAIARDILDSGRALARMQAIIAAQGGKAFDHNHPRLGALHFEVCAPADGVVAGIDNQQIA 460
                                           ************************************************************************* PP

                             TIGR02645 434 riareaGaPedkgaGvklhvkvgdkvkkGdplytiyaeseekldkaialarale 487
                                           riar+aGaP+ +gaGv l  k+gd v  G+ply+++a+ +  l+ a ++ ++ +
  NCBI__GCF_001298675.1:WP_082366649.1 461 RIARLAGAPKVQGAGVDLLCKLGDAVVSGQPLYRVHADFSADLEFARQACAQGS 514
                                           *******************************************99987776655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (493 nodes)
Target sequences:                          1  (531 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: 00:00:00.00
# Mc/sec: 33.12
//
[ok]

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

Links

Downloads

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:

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:

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:

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:

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