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.
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:
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