Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_086510460.1 BZY95_RS13595 triose-phosphate isomerase
Query= BRENDA::P0A858 (255 letters) >NCBI__GCF_002151265.1:WP_086510460.1 Length = 249 Score = 228 bits (581), Expect = 9e-65 Identities = 123/249 (49%), Positives = 157/249 (63%), Gaps = 1/249 (0%) Query: 1 MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60 MR PL+ GNWK+NGS +V E ++ A V + PP Y+D A+R EG+ I Sbjct: 1 MRTPLIAGNWKMNGSAALVEEFGHRFAEKTLP-ASLDVVVLPPFPYLDAARRAFEGTPIR 59 Query: 61 LGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG 120 LGAQ ++ SGA TGE S MLK+ G +Y + GHSERR ++E DE + + G Sbjct: 60 LGAQTLNPLHSGARTGEVSGRMLKEFGVEYALAGHSERRQLYREDDEAVLDRLLAALNVG 119 Query: 121 LTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATP 180 +TP+LC+GET E +AGKT EV RQ+ V+ E VIAYEPVWAIGTG++ATP Sbjct: 120 ITPILCVGETLEERDAGKTMEVVLRQVGYVMARLEPDQRERVVIAYEPVWAIGTGRTATP 179 Query: 181 AQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKAD 240 QAQ V IR++ A D +A + + YGGS+NA NAAEL AQPDIDG LVGGASLK D Sbjct: 180 EQAQEVMAGIREYQAGYDRALAAGLRLLYGGSMNADNAAELLAQPDIDGGLVGGASLKVD 239 Query: 241 AFAVIVKAA 249 F I ++A Sbjct: 240 DFLAICQSA 248 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: 179 Number of extensions: 2 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: 255 Length of database: 249 Length adjustment: 24 Effective length of query: 231 Effective length of database: 225 Effective search space: 51975 Effective search space used: 51975 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 WP_086510460.1 BZY95_RS13595 (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.2464.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-61 194.0 0.0 1.9e-61 193.8 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086510460.1 BZY95_RS13595 triose-phosphate i Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086510460.1 BZY95_RS13595 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 193.8 0.0 1.9e-61 1.9e-61 1 228 [] 5 239 .. 5 239 .. 0.95 Alignments for each domain: == domain 1 score: 193.8 bits; conditional E-value: 1.9e-61 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGa 68 l+ +n+K+n+s ve+ + ae+ + +a v+v ppf +ld ++++ e + i+++Aq ++ +sGa lcl|NCBI__GCF_002151265.1:WP_086510460.1 5 LIAGNWKMNGSAALVEEFGHRFAEK-TLPASLDVVVLPPFPYLDAARRAFEgTPIRLGAQTLNPLHSGA 72 689************9999999887.467899*******************999*************** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinn 137 tGe+s mlk++G+++ l gHsErR l +e de + ++ + + g+++++Cvgetleer+a++t+++ lcl|NCBI__GCF_002151265.1:WP_086510460.1 73 RTGEVSGRMLKEFGVEYALAGHSERRQLYREDDEAVLDRLLAALNVGITPILCVGETLEERDAGKTMEV 141 ********************************************************************* PP TIGR00419 138 vattaaaaA.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGa 199 v+++ + + e +v+A+EPv++iGtG+++++ +a++v + +r++ + ++ +a r+lyG+ lcl|NCBI__GCF_002151265.1:WP_086510460.1 142 VLRQVGYVMarlepdqRERVVIAYEPVWAIGTGRTATPEQAQEVMAGIREYQAGYDRALAAGLRLLYGG 210 ***99855448777777778************************************************* PP TIGR00419 200 svtaaedaelaaqldvdGvLlasavlkae 228 s++a ++ael aq+d+dG L+++a+lk + lcl|NCBI__GCF_002151265.1:WP_086510460.1 211 SMNADNAAELLAQPDIDGGLVGGASLKVD 239 **************************975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (249 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.31 // [ok]
This GapMind analysis is from Sep 24 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