Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate Pf6N2E2_3356 Triosephosphate isomerase (EC 5.3.1.1)
Query= BRENDA::P0A858 (255 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3356 Length = 247 Score = 229 bits (584), Expect = 4e-65 Identities = 122/246 (49%), Positives = 161/246 (65%), Gaps = 2/246 (0%) Query: 5 LVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIMLGAQ 64 +V GNWK++G+R V EL+ LR LA +G VA+ PP +YI+ +G I +GAQ Sbjct: 1 MVAGNWKMHGTRASVAELIKGLR-HLALPSGVDVAVFPPCLYINQVVDGLKGKSISVGAQ 59 Query: 65 NVDL-NLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQGLTP 123 N + ++ GA TGE + + L D G ++IGHSERR E D+ + +KF+ + GL P Sbjct: 60 NSAVESMQGALTGEIAPSQLVDAGCSLVLIGHSERRQIMGEQDKALIRKFSAAQACGLIP 119 Query: 124 VLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATPAQA 183 VLC+GET + EAGKT EV RQ+ +++ G AF AVIAYEPVWAIGTG +A+P QA Sbjct: 120 VLCVGETREQREAGKTLEVVGRQLGGIIEELGVDAFAKAVIAYEPVWAIGTGLTASPQQA 179 Query: 184 QAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKADAFA 243 Q VH IR +A ++ +A V + YGGSV A+NAAELF PDIDG L+GGASL AD F Sbjct: 180 QDVHAAIRAQLAAENSEVARGVRLLYGGSVKAANAAELFGMPDIDGGLIGGASLNADEFG 239 Query: 244 VIVKAA 249 I +AA Sbjct: 240 AICRAA 245 Lambda K H 0.316 0.130 0.366 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: 176 Number of extensions: 7 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: 255 Length of database: 247 Length adjustment: 24 Effective length of query: 231 Effective length of database: 223 Effective search space: 51513 Effective search space used: 51513 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: 41 (21.6 bits) S2: 46 (22.3 bits)
Align candidate Pf6N2E2_3356 (Triosephosphate isomerase (EC 5.3.1.1))
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.13436.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-67 211.5 0.8 8.6e-67 211.3 0.8 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3356 Triosephosphate isomerase (EC 5. Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3356 Triosephosphate isomerase (EC 5.3.1.1) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 211.3 0.8 8.6e-67 8.6e-67 1 228 [] 1 236 [. 1 236 [. 0.94 Alignments for each domain: == domain 1 score: 211.3 bits; conditional E-value: 8.6e-67 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvda 63 +v +n+K+++++ +v++++ l+ ++a ++gv vav pp ++++ v+d ++ i+v+Aqn + lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3356 1 MVAGNWKMHGTRASVAELIKGLR-HLALPSGVDVAVFPPCLYINQVVDGLKgKSISVGAQNSAV 63 699******************98.69*************************999*******988 PP TIGR00419 64 vk.sGaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetl 126 + +Ga tGei l+d+G+ vligHsErR ++ e d+ + k++ +++ gl +v+Cvget lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3356 64 ESmQGALTGEIAPSQLVDAGCSLVLIGHSERRQIMGEQDKALIRKFSAAQACGLIPVLCVGETR 127 6538************************************************************ PP TIGR00419 127 eereaartinnvattaaaaA.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlk 183 e+rea++t+++v ++ + + + ++v+A+EPv++iGtG ++s+ +a+ v++ +r l+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3356 128 EQREAGKTLEVVGRQLGGIIeelgvdaFAKAVIAYEPVWAIGTGLTASPQQAQDVHAAIRAQLA 191 ****88888877766655544444444************************************* PP TIGR00419 184 kvskevaesvrvlyGasvtaaedaelaaqldvdGvLlasavlkae 228 + eva+ vr+lyG+sv+aa++ael+ +d+dG L+++a+l a+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3356 192 AENSEVARGVRLLYGGSVKAANAAELFGMPDIDGGLIGGASLNAD 236 ******************************************997 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: 10.01 // [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