Align Pyrimidine-nucleoside phosphorylase; PYNP; Py-NPase; EC 2.4.2.2 (characterized)
to candidate WP_050654871.1 C1M55_RS10330 thymidine phosphorylase
Query= SwissProt::P77836 (433 letters) >NCBI__GCF_002893965.1:WP_050654871.1 Length = 431 Score = 358 bits (918), Expect = e-103 Identities = 199/411 (48%), Positives = 267/411 (64%), Gaps = 14/411 (3%) Query: 4 VDLIEKKRDGHALTKEEIQFIIEGYTKGDIPDYQMSALAMAIFFRGMNEEETAELTMAMV 63 V +I KRDG L+ EI +I++ +T+G + D QMSALAMAI+FRGM+ ET T AM+ Sbjct: 5 VSIIGAKRDGRELSGTEIDWIVQAFTEGVVGDEQMSALAMAIYFRGMSRAETGRWTEAMI 64 Query: 64 HSGDTIDLSRIEGIKVDKHSTGGVGDTTTLVLGPLVASVGVPVAKMSGRGLGHTGGTIDK 123 SG +D S + VDKHSTGGVGD TL L PLVA+ G+ V ++SGRGLGHTGGT+DK Sbjct: 65 ESGGRMDFSDLPLPTVDKHSTGGVGDKITLPLAPLVAACGLAVPQLSGRGLGHTGGTLDK 124 Query: 124 LESVPGFHVEITNDEFIDLVNKNKIAVV--GQSGNLTPADKKLYALRDVTATVNSIPLIA 181 LE++PG+ E+T E +D+++ KI V NL PADKKLYALRDVT TV SIPLIA Sbjct: 125 LEAIPGWRAELTATEMVDILSDPKIGAVICAAGANLAPADKKLYALRDVTGTVESIPLIA 184 Query: 182 SSIMSKKIAAGADAIVLDVKTGVGAFMKDLNDAKALAKAMVDIGNRVGRKTMAIISDMSQ 241 SSIMSKKIA G A+VLDVK G GAFMKDL DA+ LA+ MV++GN G +T A+I+ M Sbjct: 185 SSIMSKKIAEGTGALVLDVKVGSGAFMKDLGDARELARTMVELGNDAGVRTSALITGMDT 244 Query: 242 PLGYAIGNALEVKEAIDTLKGEGPEDFQELCLVLGSHMVYLAEKASSLEEARHMLEKAMK 301 PLG GNALEV+E+++ L G GP D EL LVL M+ A ++ A + Sbjct: 245 PLGLTAGNALEVRESVEVLAGGGPSDVVELTLVLAREML-SAAGIDGIDPA-----DKLS 298 Query: 302 DGSALQTFKTFLAAQGGDASVVDDPSKLPQAKYIIELEAKEDGYVSEIVADAVGTAAMWL 361 DG+A+ ++ +AAQGGD + LP A++ + A DG ++ + A AVG AA L Sbjct: 299 DGTAMDRWRAMIAAQGGDPH-----ATLPTARHSDVVTADRDGVLTRLDAMAVGIAAWKL 353 Query: 362 GAGRATKESTIDLAVGLVLRKKVGDAVKKGESLVTIYSNR-EQVDDVKQKL 411 GAGR + + G+ + K GD V+ G+ L+T++++ E+ D ++ L Sbjct: 354 GAGRERQGEAVQAGAGIEMHAKPGDVVRAGQKLMTLHTDTPERFDAARRSL 404 Lambda K H 0.315 0.133 0.361 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: 494 Number of extensions: 29 Number of successful extensions: 4 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: 433 Length of database: 431 Length adjustment: 32 Effective length of query: 401 Effective length of database: 399 Effective search space: 159999 Effective search space used: 159999 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 51 (24.3 bits)
Align candidate WP_050654871.1 C1M55_RS10330 (thymidine phosphorylase)
to HMM TIGR02644 (pdp: pyrimidine-nucleoside phosphorylase (EC 2.4.2.2))
# 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/TIGR02644.hmm # target sequence database: /tmp/gapView.1968806.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02644 [M=417] Accession: TIGR02644 Description: Y_phosphoryl: pyrimidine-nucleoside 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-168 546.5 0.2 2.2e-168 546.3 0.2 1.0 1 NCBI__GCF_002893965.1:WP_050654871.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002893965.1:WP_050654871.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 546.3 0.2 2.2e-168 2.2e-168 2 410 .. 5 404 .. 4 411 .. 0.98 Alignments for each domain: == domain 1 score: 546.3 bits; conditional E-value: 2.2e-168 TIGR02644 2 veiiekKrdgkklseeeinflingytkgeiadyQisallmaiyfkgldkeEtlalTkamvesGevldlselkk 74 v+ii Krdg++ls +ei+++++++t+g + d+Q+sal+maiyf+g++++Et ++T+am+esG ++d+s+l+ NCBI__GCF_002893965.1:WP_050654871.1 5 VSIIGAKRDGRELSGTEIDWIVQAFTEGVVGDEQMSALAMAIYFRGMSRAETGRWTEAMIESGGRMDFSDLPL 77 789********************************************************************** PP TIGR02644 75 ikvDKHStGGvGDkvsLvlaPlvaalgvkvaklSGRgLghTGGTlDKLesipGfktelseeefieivkk..vg 145 ++vDKHStGGvGDk++L+laPlvaa+g++v++lSGRgLghTGGTlDKLe+ipG+++el+ e+++i+++ +g NCBI__GCF_002893965.1:WP_050654871.1 78 PTVDKHSTGGVGDKITLPLAPLVAACGLAVPQLSGRGLGHTGGTLDKLEAIPGWRAELTATEMVDILSDpkIG 150 *******************************************************************965599 PP TIGR02644 146 laiigqtkdlapaDkklYalRdvtgTvdslpLiasSilsKKlaagadalvlDvkvGkGaFmktleeakeLake 218 ++i++++++lapaDkklYalRdvtgTv+s+pLiasSi+sKK+a+g+ alvlDvkvG+GaFmk+l +a+eLa++ NCBI__GCF_002893965.1:WP_050654871.1 151 AVICAAGANLAPADKKLYALRDVTGTVESIPLIASSIMSKKIAEGTGALVLDVKVGSGAFMKDLGDARELART 223 9************************************************************************ PP TIGR02644 219 lveigkkagrkvvalltdmnepLgkaiGNalEvkeavevLkgegpadlkelvlalaaemlllaklakteeeak 291 +ve+g++ag++++al+t m++pLg ++GNalEv+e+vevL+g gp+d++el+l la+eml +a+++ NCBI__GCF_002893965.1:WP_050654871.1 224 MVELGNDAGVRTSALITGMDTPLGLTAGNALEVRESVEVLAGGGPSDVVELTLVLAREMLSAAGIDG------ 290 ******************************************************************8...... PP TIGR02644 292 ekleevlesgkalekfkefveaqgGdlevlkeekklakakkkeevkaeksgvieeidaeelgliavelgaGRa 364 + +++l++g+a+++++++++aqgGd+ +++l++a+++ v+a+++gv++++da+++g++a++lgaGR+ NCBI__GCF_002893965.1:WP_050654871.1 291 IDPADKLSDGTAMDRWRAMIAAQGGDP-----HATLPTARHSDVVTADRDGVLTRLDAMAVGIAAWKLGAGRE 358 788999********************8.....6789************************************* PP TIGR02644 365 kkedkidleaGielekkvgdkvkkgdllltlyssdeekaeeaakal 410 ++ + ++ aGie+++k gd v++g++l+tl+++++e++++a++ l NCBI__GCF_002893965.1:WP_050654871.1 359 RQGEAVQAGAGIEMHAKPGDVVRAGQKLMTLHTDTPERFDAARRSL 404 **************************************99998776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (417 nodes) Target sequences: 1 (431 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: 00:00:00.01 # Mc/sec: 17.34 // [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