Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate 3608685 Dshi_2078 Triose-phosphate isomerase (RefSeq)
Query= SwissProt::Q8L1Z5 (254 letters) >FitnessBrowser__Dino:3608685 Length = 247 Score = 231 bits (590), Expect = 8e-66 Identities = 123/243 (50%), Positives = 160/243 (65%), Gaps = 4/243 (1%) Query: 6 RPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGGENILL 65 R AGNWKMNG +L E AI A ++D E L+C PATLL+ G + + Sbjct: 3 RKLAAGNWKMNGLRAALAEAEAITAAAAADGP---EVLLCPPATLLAPMAAQAEGTALQI 59 Query: 66 GGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWRAGL 125 GGQ CH G +TG +SA ML++AGAS+VI+GHSERR E DA VRA+ AAW+AGL Sbjct: 60 GGQYCHPAPSGAHTGHVSAPMLRDAGASYVIVGHSERRQDDGERDADVRAQTLAAWQAGL 119 Query: 126 VALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATSADV 185 A++CVGET ER + L ++ QL GS+PD AT N+++AYEPVWA+GTG + + Sbjct: 120 TAIVCVGETEAERDAANTLAIIGGQLAGSIPDTATGANLVVAYEPVWAIGTGRVPSVDQI 179 Query: 186 AEVHAFIHHKMHSRFGD-EGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKAIDF 244 EVH FI ++ RFG+ G +RLLYGGSVKP A E+ + ++V+GAL+GGASLKA DF Sbjct: 180 GEVHDFIRARLEQRFGEGVGRSVRLLYGGSVKPGIAAEIFAVSNVDGALVGGASLKAADF 239 Query: 245 LTI 247 I Sbjct: 240 TGI 242 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: 247 Number of extensions: 10 Number of successful extensions: 3 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: 247 Length adjustment: 24 Effective length of query: 230 Effective length of database: 223 Effective search space: 51290 Effective search space used: 51290 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 3608685 Dshi_2078 (Triose-phosphate isomerase (RefSeq))
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.2385.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-51 161.4 0.4 1.7e-51 161.2 0.4 1.0 1 lcl|FitnessBrowser__Dino:3608685 Dshi_2078 Triose-phosphate isome Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3608685 Dshi_2078 Triose-phosphate isomerase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 161.2 0.4 1.7e-51 1.7e-51 3 227 .. 7 236 .. 5 237 .. 0.90 Alignments for each domain: == domain 1 score: 161.2 bits; conditional E-value: 1.7e-51 TIGR00419 3 iinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGeisAeml 78 +n+K+n+ + ++ a + a +g ev + pp l ++ ++e + +q++ q ++ sGa+tG++sA ml lcl|FitnessBrowser__Dino:3608685 7 AGNWKMNGLRAALAEAEA-I-TAAAAADGPEVLLCPPATLLAPMAAQAEgTALQIGGQYCHPAPSGAHTGHVSAPML 81 68*****99888776433.3.3456778999999999999988888888799************************* PP TIGR00419 79 kdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaaA.....lepd 150 +d+Ga +v++gHsErR e d + ++ + + gl+++vCvget++er+aa+t+ + + a + lcl|FitnessBrowser__Dino:3608685 82 RDAGASYVIVGHSERRQDDGERDADVRAQTLAAWQAGLTAIVCVGETEAERDAANTLAIIGGQLAGSIpdtatGANL 158 ****************998888877999999999***********************99988766433344447789 PP TIGR00419 151 vvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaedaelaaqldvdGvLlasavlk 226 vvA+EPv++iGtG++ s + +v++++r l++ + v +svr+lyG+sv+ + +ae +a +vdG+L+++a+lk lcl|FitnessBrowser__Dino:3608685 159 VVAYEPVWAIGTGRVPSVDQIGEVHDFIRARLEQrFGEGVGRSVRLLYGGSVKPGIAAEIFAVSNVDGALVGGASLK 235 ********************************9989999************************************** PP TIGR00419 227 a 227 a lcl|FitnessBrowser__Dino:3608685 236 A 236 8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (247 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: 5.68 // [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