Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate CCNA_01970 CCNA_01970 triosephosphate isomerase
Query= SwissProt::Q8L1Z5 (254 letters) >FitnessBrowser__Caulo:CCNA_01970 Length = 253 Score = 223 bits (569), Expect = 2e-63 Identities = 117/242 (48%), Positives = 158/242 (65%), Gaps = 1/242 (0%) Query: 6 RPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGGENILL 65 RP IAGNWKMNG +L E RA+AA + + A+ PATLL R + G ++L Sbjct: 9 RPLIAGNWKMNGLSVALDEARAVAAALEAKPPAARVAIF-PPATLLHRLSQAVEGAHLLT 67 Query: 66 GGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWRAGL 125 GGQ+CH G +TGD+SA M+ +AG S VI GHSERRT + E+ A V K +AA AGL Sbjct: 68 GGQDCHGKSSGAHTGDVSAEMVADAGGSLVICGHSERRTDHGETSAQVAGKAEAAAAAGL 127 Query: 126 VALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATSADV 185 ++CVGETLE R++ + + + Q+ SLP + +AYEP+WA+GTG TA+ ++ Sbjct: 128 EPIVCVGETLETREAGQAVSFVVSQVRDSLPTSLAGKAFSVAYEPLWAIGTGRTASVDNI 187 Query: 186 AEVHAFIHHKMHSRFGDEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKAIDFL 245 E+HA I ++ SRF ++G + +LYGGSVKP NA E+L+ V GAL+GGASLKA DFL Sbjct: 188 VEMHAAIRAELVSRFCEQGRTVLILYGGSVKPENAREILAAPEVGGALVGGASLKAKDFL 247 Query: 246 TI 247 I Sbjct: 248 AI 249 Lambda K H 0.320 0.137 0.403 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: 218 Number of extensions: 8 Number of successful extensions: 2 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: 254 Length of database: 253 Length adjustment: 24 Effective length of query: 230 Effective length of database: 229 Effective search space: 52670 Effective search space used: 52670 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: 47 (22.7 bits)
Align candidate CCNA_01970 CCNA_01970 (triosephosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))
# 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/TIGR00419.hmm # target sequence database: /tmp/gapView.23540.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00419 [M=228] Accession: TIGR00419 Description: tim: triose-phosphate isomerase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-51 160.5 1.5 3.3e-51 160.3 1.5 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_01970 CCNA_01970 triosephosphate isome Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_01970 CCNA_01970 triosephosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 160.3 1.5 3.3e-51 3.3e-51 1 228 [] 11 244 .. 11 244 .. 0.92 Alignments for each domain: == domain 1 score: 160.3 bits; conditional E-value: 3.3e-51 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 l+ +n+K+n+ ++ a a+ a++ va+ pp l++++++ve +++ + q+++ ++sGa+tG+ lcl|FitnessBrowser__Caulo:CCNA_01970 11 LIAGNWKMNGLSVALDEARAVAAALEAKPPAARVAIFPPATLLHRLSQAVEgAHLLTGGQDCHGKSSGAHTGD 83 689******98888887777777777999**********************99******************** PP TIGR00419 73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaa.. 143 +sAem++d+G v+ gHsErR+ + e++ ++ k + + gl+++vCvgetle rea++ + v + lcl|FitnessBrowser__Caulo:CCNA_01970 84 VSAEMVADAGGSLVICGHSERRTDHGETSAQVAGKAEAAAAAGLEPIVCVGETLETREAGQAVSFVVSQVRds 156 ***********************************************************99999888775411 PP TIGR00419 144 ...aaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaql 213 A + vA+EP ++iGtG+++s + ++++ +r l e + v +lyG+sv+ +++ e a + lcl|FitnessBrowser__Caulo:CCNA_01970 157 lptSLAGKAFSVAYEPLWAIGTGRTASVDNIVEMHAAIRAELVSRFCEQGRTVLILYGGSVKPENAREILAAP 229 11144566678****************************9998888899999********************* PP TIGR00419 214 dvdGvLlasavlkae 228 +v G+L+++a+lka+ lcl|FitnessBrowser__Caulo:CCNA_01970 230 EVGGALVGGASLKAK 244 *************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (253 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: 00:00:00.00 # Mc/sec: 5.80 // [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