Align thymidine phosphorylase (EC 2.4.2.4) (characterized)
to candidate 6936792 Sama_0974 thymidine phosphorylase (RefSeq)
Query= BRENDA::Q7CP66 (440 letters) >FitnessBrowser__SB2B:6936792 Length = 443 Score = 601 bits (1549), Expect = e-176 Identities = 295/438 (67%), Positives = 358/438 (81%) Query: 1 MFLAQEIIRKKRDGHALSDEEIRFFINGIRDNTISEGQIAALAMTIFFHDMTMPERVSLT 60 MFLAQEIIRKKR+ ALS EEI+FF+ GI DN++SEGQIAAL M ++F+DMTM ER++LT Sbjct: 1 MFLAQEIIRKKRNAEALSKEEIQFFVKGITDNSVSEGQIAALGMAVYFNDMTMDERIALT 60 Query: 61 MAMRDSGTVLDWKSLNLNGPIVDKHSTGGVGDVTSLMLGPMVAACGGYVPMISGRGLGHT 120 AMRDSGTVL+W SL LNGP++DKHSTGGVGDV SLMLGPM AACGGYVPMISGRGLGHT Sbjct: 61 TAMRDSGTVLNWDSLGLNGPVIDKHSTGGVGDVISLMLGPMAAACGGYVPMISGRGLGHT 120 Query: 121 GGTLDKLEAIPGFDIFPDDNRFREIIQDVGVAIIGQTSSLAPADKRFYATRDITATVDSI 180 GGTLDK +AIPG+ P FR+++++ GVAIIGQT L PADKRFY+ RD TATV+SI Sbjct: 121 GGTLDKFDAIPGYQTEPSSELFRKVVKEAGVAIIGQTGDLVPADKRFYSIRDNTATVESI 180 Query: 181 PLITGSILAKKLAEGLDALVMDVKVGSGAFMPTYELSEALAEAIVGVANGAGVRTTALLT 240 LIT SIL+KKLA GLDAL MDVKVGSGAFMPTYE S LA +I VANGAG +TTALLT Sbjct: 181 SLITASILSKKLAAGLDALAMDVKVGSGAFMPTYEASLELARSITAVANGAGTKTTALLT 240 Query: 241 DMNQVLASSAGNAVEVREAVQFLTGEYRNPRLFDVTMALCVEMLISGQLAKDDAEARAKL 300 DMNQVLAS AGNA+EV+EAV FLTG+YRNPRL++VTM LC EML+ G LA +DA+AR KL Sbjct: 241 DMNQVLASCAGNALEVKEAVDFLTGKYRNPRLYEVTMGLCAEMLVLGGLAANDADARTKL 300 Query: 301 QAVLDNGKAAEVFGRMVAAQKGPSDFVENYDKYLPTAMLSKAVYADTEGFISAMDTRALG 360 VLDNG+AAE+FG+MV+ GP+DFVE+YDKYLP A + + VYA+ +GF +M TR LG Sbjct: 301 NTVLDNGRAAEIFGKMVSGLGGPADFVESYDKYLPKASIIRPVYAERDGFAYSMVTRELG 360 Query: 361 MAVVSMGGGRRQASDTIDYSVGFTDMARLGDSIDGQRPLAVIHAKDEASWQEAAKAVKAA 420 +AVV++GGGRR+ D +DYSVG +++ LG I+ PLAVIHA+ EA+++EAA+AV+ A Sbjct: 361 LAVVTLGGGRRKPGDALDYSVGLSNVCALGQPINKDTPLAVIHAQSEAAFEEAARAVRGA 420 Query: 421 IILDDKAPASTPSVYRRI 438 I + DK P TP +Y+ + Sbjct: 421 ITVSDKQPEKTPEIYQYV 438 Lambda K H 0.319 0.134 0.377 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: 609 Number of extensions: 14 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: 440 Length of database: 443 Length adjustment: 32 Effective length of query: 408 Effective length of database: 411 Effective search space: 167688 Effective search space used: 167688 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 (21.7 bits) S2: 51 (24.3 bits)
Align candidate 6936792 Sama_0974 (thymidine phosphorylase (RefSeq))
to HMM TIGR02643 (deoA: 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/TIGR02643.hmm # target sequence database: /tmp/gapView.15729.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02643 [M=437] Accession: TIGR02643 Description: T_phosphoryl: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-224 729.7 3.6 6.8e-224 729.5 3.6 1.0 1 lcl|FitnessBrowser__SB2B:6936792 Sama_0974 thymidine phosphorylas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6936792 Sama_0974 thymidine phosphorylase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 729.5 3.6 6.8e-224 6.8e-224 1 436 [. 2 437 .. 2 438 .. 1.00 Alignments for each domain: == domain 1 score: 729.5 bits; conditional E-value: 6.8e-224 TIGR02643 1 llpqeiirkkrdglslsdeeiaafvegvtddsvsegqiaalamavyfngleldekvaltlamrdsGdvldwkdldln 77 +l+qeiirkkr++++ls+eei+ fv+g+td+svsegqiaal mavyfn++++de++alt amrdsG+vl+w +l ln lcl|FitnessBrowser__SB2B:6936792 2 FLAQEIIRKKRNAEALSKEEIQFFVKGITDNSVSEGQIAALGMAVYFNDMTMDERIALTTAMRDSGTVLNWDSLGLN 78 79*************************************************************************** PP TIGR02643 78 gPvvdkhstGGvGdvvslmlaPivaacGgyvPmisGrGlGhtGGtldkleaiPGydvaPdeelfrkvvkdvGvaiiG 154 gPv+dkhstGGvGdv+slml+P+ aacGgyvPmisGrGlGhtGGtldk++aiPGy++ P++elfrkvvk++GvaiiG lcl|FitnessBrowser__SB2B:6936792 79 GPVIDKHSTGGVGDVISLMLGPMAAACGGYVPMISGRGLGHTGGTLDKFDAIPGYQTEPSSELFRKVVKEAGVAIIG 155 ***************************************************************************** PP TIGR02643 155 qtadlaPadkrlyairdvtatvesiplitasilskklaaGldalvldvkvGnGafmesleeseelarslvevangaG 231 qt+dl Padkr+y+ird tatvesi+litasilskklaaGldal++dvkvG+Gafm+++e s elars+ vangaG lcl|FitnessBrowser__SB2B:6936792 156 QTGDLVPADKRFYSIRDNTATVESISLITASILSKKLAAGLDALAMDVKVGSGAFMPTYEASLELARSITAVANGAG 232 ***************************************************************************** PP TIGR02643 232 vrttalitdmnqalasaaGnavevreavdfltGekrdkrleevtlalaaellvsgklaadeaeaeakleavlesGra 308 +ttal+tdmnq+las+aGna+ev+eavdfltG++r++rl evt+ l+ae+lv g+laa++a+a++kl++vl++Gra lcl|FitnessBrowser__SB2B:6936792 233 TKTTALLTDMNQVLASCAGNALEVKEAVDFLTGKYRNPRLYEVTMGLCAEMLVLGGLAANDADARTKLNTVLDNGRA 309 ***************************************************************************** PP TIGR02643 309 aerfarmvaalgGPadfvekpekylakaaiakavkaaregylseidtrelGlavvalGGGrrkaddkldlsvGltdl 385 ae+f++mv+ lgGPadfve ++kyl+ka+i+++v+a+r+g+ ++ trelGlavv+lGGGrrk+ d ld+svGl+++ lcl|FitnessBrowser__SB2B:6936792 310 AEIFGKMVSGLGGPADFVESYDKYLPKASIIRPVYAERDGFAYSMVTRELGLAVVTLGGGRRKPGDALDYSVGLSNV 386 ***************************************************************************** PP TIGR02643 386 lelGekvekeeplavvhaadeedaeeaakavkkalkiadeaPeeakvvler 436 lG+ ++k++plav+ha++e+ +eeaa+av+ a++++d++Pe+++ +++ lcl|FitnessBrowser__SB2B:6936792 387 CALGQPINKDTPLAVIHAQSEAAFEEAARAVRGAITVSDKQPEKTPEIYQY 437 ***********************************************9985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (437 nodes) Target sequences: 1 (443 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 8.34 // [ok]
This GapMind analysis is from Sep 17 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