Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_085770362.1 B1812_RS03470 triose-phosphate isomerase
Query= SwissProt::Q8L1Z5 (254 letters) >NCBI__GCF_002117405.1:WP_085770362.1 Length = 252 Score = 252 bits (643), Expect = 6e-72 Identities = 128/247 (51%), Positives = 165/247 (66%) Query: 6 RPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGGENILL 65 RP +AGNWKMNG +L E+ AIA G + L + LIC PATLL+ A L G ++ L Sbjct: 6 RPLVAGNWKMNGLHAALSEIDAIATGFDAGLREKIDLLICPPATLLAAAAARLEGTDVAL 65 Query: 66 GGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWRAGL 125 GGQ+CH G +TGD+SA ML +AGA VI+GHSERR + ESD +V AK +AA AGL Sbjct: 66 GGQDCHAQVSGAHTGDVSALMLADAGARFVIVGHSERRADHGESDGLVLAKARAALSAGL 125 Query: 126 VALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATSADV 185 + ++C+GET ER + + V+ Q+ GSLP A E +++AYEPVWA+GTG T T DV Sbjct: 126 MPIVCIGETRGERDAGQAESVVAAQIAGSLPPEAPPERLVVAYEPVWAIGTGLTPTPQDV 185 Query: 186 AEVHAFIHHKMHSRFGDEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKAIDFL 245 A +H F ++ + +GA R+LYGGSVKP NA ELL + V+GAL+GGASLKA DFL Sbjct: 186 ARMHGFARQRIEALGPGKGAATRILYGGSVKPENARELLRVSDVDGALVGGASLKAKDFL 245 Query: 246 TICDVYR 252 I YR Sbjct: 246 AIAAAYR 252 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: 224 Number of extensions: 8 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: 254 Length of database: 252 Length adjustment: 24 Effective length of query: 230 Effective length of database: 228 Effective search space: 52440 Effective search space used: 52440 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: 46 (22.3 bits)
Align candidate WP_085770362.1 B1812_RS03470 (triose-phosphate 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.aa/TIGR00419.hmm # target sequence database: /tmp/gapView.27847.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.5e-53 165.7 0.0 8.6e-53 165.5 0.0 1.0 1 lcl|NCBI__GCF_002117405.1:WP_085770362.1 B1812_RS03470 triose-phosphate i Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002117405.1:WP_085770362.1 B1812_RS03470 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 165.5 0.0 8.6e-53 8.6e-53 1 228 [] 8 242 .. 8 242 .. 0.93 Alignments for each domain: == domain 1 score: 165.5 bits; conditional E-value: 8.6e-53 TIGR00419 1 lviinfKlnesvgkvelevaklae..evaseagvevavappfvdldvvkdeve.seiqvaAqnvdavks 66 lv +n+K+n+ + e+ +a + ++++ + + pp l ++ ++e +++ ++ q+++a+ s lcl|NCBI__GCF_002117405.1:WP_085770362.1 8 LVAGNWKMNGL-HAALSEIDAIATgfDAGLREKIDLLICPPATLLAAAAARLEgTDVALGGQDCHAQVS 75 799*****985.666677888887677788999********************99************** PP TIGR00419 67 GaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaarti 135 Ga+tG++sA ml+d+Ga++v++gHsErR+ + e+d l+ +k + gl+++vC+get er+a++ lcl|NCBI__GCF_002117405.1:WP_085770362.1 76 GAHTGDVSALMLADAGARFVIVGHSERRADHGESDGLVLAKARAALSAGLMPIVCIGETRGERDAGQAE 144 *****************************************************************9987 PP TIGR00419 136 nnvattaaaaA.....lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGa 199 +va + a e vvA+EPv++iGtG + ++ + ++++ r+ ++ + +r+lyG+ lcl|NCBI__GCF_002117405.1:WP_085770362.1 145 SVVAAQIAGSLppeapPERLVVAYEPVWAIGTGLTPTPQDVARMHGFARQRIEALGPGKGAATRILYGG 213 77776655443566567788************************************************* PP TIGR00419 200 svtaaedaelaaqldvdGvLlasavlkae 228 sv+ +++ el dvdG+L+++a+lka+ lcl|NCBI__GCF_002117405.1:WP_085770362.1 214 SVKPENARELLRVSDVDGALVGGASLKAK 242 ***************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (252 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: 7.14 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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