Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_008485428.1 B3C1_RS13285 triose-phosphate isomerase
Query= BRENDA::P0A858 (255 letters) >NCBI__GCF_000299915.1:WP_008485428.1 Length = 250 Score = 263 bits (671), Expect = 3e-75 Identities = 130/249 (52%), Positives = 173/249 (69%) Query: 1 MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60 MR PLVMGNWKL+GS+ V +L+ L + V G +A+ PP +++ A+R S I Sbjct: 1 MRRPLVMGNWKLHGSKASVEKLLVELMVKANEVEGVEIAVCPPLVFVGQAERLLRYSQIA 60 Query: 61 LGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG 120 LGAQN+D+N GAFTGE +A ML + G +Y+++GHSERR H E+D+L+A+KF +K G Sbjct: 61 LGAQNIDVNRQGAFTGEVAADMLGEFGVRYVLVGHSERRAMHHENDDLVARKFEAVKAAG 120 Query: 121 LTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATP 180 L PVLC+GET+AE G+T++V Q+ AV+K G AF+ AV+AYEPVWAIG+G++A+P Sbjct: 121 LIPVLCVGETQAERNNGETKDVIGHQLQAVVKRCGRKAFDNAVVAYEPVWAIGSGQAASP 180 Query: 181 AQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKAD 240 AQ VH+FIR +A D A+ + I YGGSV ASNA LF D+DGALVGGASL A Sbjct: 181 VDAQKVHEFIRAQVAAQDPASAQALRILYGGSVKASNAQALFMMDDVDGALVGGASLDAQ 240 Query: 241 AFAVIVKAA 249 F+ I AA Sbjct: 241 EFSGIFNAA 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: 183 Number of extensions: 3 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: 255 Length of database: 250 Length adjustment: 24 Effective length of query: 231 Effective length of database: 226 Effective search space: 52206 Effective search space used: 52206 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_008485428.1 B3C1_RS13285 (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.2765142.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-74 235.7 2.4 3.3e-74 235.5 2.4 1.0 1 NCBI__GCF_000299915.1:WP_008485428.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000299915.1:WP_008485428.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 235.5 2.4 3.3e-74 3.3e-74 1 227 [. 5 239 .. 5 240 .. 0.98 Alignments for each domain: == domain 1 score: 235.5 bits; conditional E-value: 3.3e-74 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 lv++n+Kl++s +ve+++ +l + +++gve+av pp v++ +++ ++ s+i ++Aqn+d++++GaftGe NCBI__GCF_000299915.1:WP_008485428.1 5 LVMGNWKLHGSKASVEKLLVELMVKANEVEGVEIAVCPPLVFVGQAERLLRySQIALGAQNIDVNRQGAFTGE 77 79*********************************************************************** PP TIGR00419 73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere.......aartinnv 138 + A+ml ++G+++vl+gHsErR++++e d+l++ k+ +k+ gl +v+Cvget++er+ ++++++v NCBI__GCF_000299915.1:WP_008485428.1 78 VAADMLGEFGVRYVLVGHSERRAMHHENDDLVARKFEAVKAAGLIPVLCVGETQAERNngetkdvIGHQLQAV 150 ********************************************************99888888888999999 PP TIGR00419 139 attaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaa 211 + + A++++vvA+EPv++iG+G+++s+ +a+ v++++r ++ ++ a+ r+lyG+sv+a++++ l++ NCBI__GCF_000299915.1:WP_008485428.1 151 VKRCGRKAFDNAVVAYEPVWAIGSGQAASPVDAQKVHEFIRAQVAAQDPASAQALRILYGGSVKASNAQALFM 223 99999999***************************************************************** PP TIGR00419 212 qldvdGvLlasavlka 227 dvdG+L+++a+l a NCBI__GCF_000299915.1:WP_008485428.1 224 MDDVDGALVGGASLDA 239 *************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (250 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: 17.20 // [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