Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate PP_4715 PP_4715 triose phosphate isomerase
Query= BRENDA::P0A858 (255 letters) >FitnessBrowser__Putida:PP_4715 Length = 251 Score = 240 bits (613), Expect = 2e-68 Identities = 129/250 (51%), Positives = 164/250 (65%), Gaps = 2/250 (0%) Query: 1 MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60 MR P+V GNWK++G+R V EL L LA +G VA+ PP ++I+ G I Sbjct: 1 MRRPMVAGNWKMHGTRASVAELTKGL-SNLALPSGVEVAVFPPALFINQVIDGLAGKEIT 59 Query: 61 LGAQNVDLNLS-GAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQ 119 +GAQN + GA TGE + L + G + ++IGHSERR E+DE++ +KFA + + Sbjct: 60 VGAQNSAVQPEQGALTGEVAPEQLVEAGCKLVLIGHSERRQIIGETDEVLNRKFAAAQAK 119 Query: 120 GLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSAT 179 GL PVLCIGET E EAGKT EV RQ+ ++++ G AF AVIAYEPVWAIGTG +AT Sbjct: 120 GLKPVLCIGETLEEREAGKTLEVVGRQLSSIIEAFGVKAFADAVIAYEPVWAIGTGLTAT 179 Query: 180 PAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKA 239 P QAQ VH IR +A DA +A +V + YGGSV A+NAAELF PDIDG L+GGASL A Sbjct: 180 PQQAQDVHAAIRGQLAAEDAEVAAKVQLLYGGSVKAANAAELFGMPDIDGGLIGGASLNA 239 Query: 240 DAFAVIVKAA 249 D F I +AA Sbjct: 240 DEFGAICRAA 249 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: 188 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: 251 Length adjustment: 24 Effective length of query: 231 Effective length of database: 227 Effective search space: 52437 Effective search space used: 52437 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 PP_4715 PP_4715 (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.carbon/TIGR00419.hmm # target sequence database: /tmp/gapView.556.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-69 220.0 2.2 2.2e-69 219.7 2.2 1.0 1 lcl|FitnessBrowser__Putida:PP_4715 PP_4715 triose phosphate isomera Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_4715 PP_4715 triose phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 219.7 2.2 2.2e-69 2.2e-69 1 228 [] 5 240 .. 5 240 .. 0.92 Alignments for each domain: == domain 1 score: 219.7 bits; conditional E-value: 2.2e-69 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdav.ksGaftGei 73 +v +n+K+++++ +v+++ l ++a ++gvevav pp ++++ v d + ei+v+Aqn ++ ++Ga tGe+ lcl|FitnessBrowser__Putida:PP_4715 5 MVAGNWKMHGTRASVAELTKGL-SNLALPSGVEVAVFPPALFINQVIDGLAgKEITVGAQNSAVQpEQGALTGEV 78 699************9877776.68************************9989********9886479******* PP TIGR00419 74 sAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinnvatt 141 e l+++G+k vligHsErR ++ e+de+++ k+a ++++glk+v+C+getleere ++r++ + + lcl|FitnessBrowser__Putida:PP_4715 79 APEQLVEAGCKLVLIGHSERRQIIGETDEVLNRKFAAAQAKGLKPVLCIGETLEEREagktlevVGRQLSSIIEA 153 *********************************************************444444444444445555 PP TIGR00419 142 aaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvd 216 ++ A+ ++v+A+EPv++iGtG ++++ +a+ v++ +r l+ ++eva +v++lyG+sv+aa++ael+ +d+d lcl|FitnessBrowser__Putida:PP_4715 154 FGVKAFADAVIAYEPVWAIGTGLTATPQQAQDVHAAIRGQLAAEDAEVAAKVQLLYGGSVKAANAAELFGMPDID 228 56666********************************************************************** PP TIGR00419 217 GvLlasavlkae 228 G L+++a+l a+ lcl|FitnessBrowser__Putida:PP_4715 229 GGLIGGASLNAD 240 *********997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (251 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: 10.28 // [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