Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_011611066.1 TERY_RS06405 triose-phosphate isomerase
Query= BRENDA::P00943 (253 letters) >NCBI__GCF_000014265.1:WP_011611066.1 Length = 241 Score = 238 bits (606), Expect = 1e-67 Identities = 125/248 (50%), Positives = 170/248 (68%), Gaps = 11/248 (4%) Query: 1 MRKPIIAGNWKMHKTLAEAVQFVEDVKGHVPPADEVISVV-CAPFLFLDRLVQAADGTDL 59 MRK IIAGNWKM+KT EA +F+E + + E VV C PF LD + + G+ + Sbjct: 1 MRKTIIAGNWKMYKTQLEAKEFLEGLMSQLTKTPEEREVVLCTPFTALDFMSKILHGSLI 60 Query: 60 KIGAQTMHFADQGAYTGEVSPVMLKDLGVTYVILGHSERRQMFAETDETVNKKVLAAFTR 119 ++GAQ +H+ D+GAYTGE+S +MLKD+GV+YVI+GHSERRQ F ETDETVN ++ AA Sbjct: 61 RLGAQNVHWEDEGAYTGEISGLMLKDVGVSYVIVGHSERRQYFGETDETVNMRLKAAQKH 120 Query: 120 GLIPIICCGESLEEREAGQTNAVVASQVEKALAGLTPEQVKQAVIAYEPIWAIGTGKSST 179 GL PI+C GE+ ++R++G+T + + SQ+ L + E + VIAYEPIWAIGTG + Sbjct: 121 GLTPILCVGETKQQRDSGETESHIFSQLANDLVDVDQENL---VIAYEPIWAIGTGDTCE 177 Query: 180 PEDANSVCGHIRSVVSRLFGPEAAEAIRIQYGGSVKPDNIRDFLAQQQIDGPLVGGASLE 239 ++AN V G IR ++ + IQYGGSVKP+N+ D +AQ++IDG LVGGASL Sbjct: 178 AKEANRVIGLIRGKLNN-------SNVTIQYGGSVKPNNVDDIMAQEEIDGALVGGASLN 230 Query: 240 PASFLQLV 247 P SF +LV Sbjct: 231 PESFSRLV 238 Lambda K H 0.318 0.134 0.389 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: 194 Number of extensions: 12 Number of successful extensions: 4 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: 253 Length of database: 241 Length adjustment: 24 Effective length of query: 229 Effective length of database: 217 Effective search space: 49693 Effective search space used: 49693 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 (21.7 bits) S2: 46 (22.3 bits)
Align candidate WP_011611066.1 TERY_RS06405 (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.aa/TIGR00419.hmm # target sequence database: /tmp/gapView.30357.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-54 170.7 0.0 2.6e-54 170.5 0.0 1.0 1 lcl|NCBI__GCF_000014265.1:WP_011611066.1 TERY_RS06405 triose-phosphate is Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000014265.1:WP_011611066.1 TERY_RS06405 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 170.5 0.0 2.6e-54 2.6e-54 1 228 [] 5 232 .. 5 232 .. 0.93 Alignments for each domain: == domain 1 score: 170.5 bits; conditional E-value: 2.6e-54 TIGR00419 1 lviinfKlnesvgkvelevaklaeevas.eagvevavappfvdldvvkdeve.seiqvaAqnvdavksG 67 ++ +n+K+ + + ++ + l ++++ +++ ev++ pf ld +++ ++ s i+++Aqnv+ + G lcl|NCBI__GCF_000014265.1:WP_011611066.1 5 IIAGNWKMYKTQLEAKEFLEGLMSQLTKtPEEREVVLCTPFTALDFMSKILHgSLIRLGAQNVHWEDEG 73 6899***9999999999*******9987256789******************999************** PP TIGR00419 68 aftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartin 136 a+tGeis mlkd+G+ +v++gHsErR ++ e+de +++++ +++ gl++++Cvget+++r++++t lcl|NCBI__GCF_000014265.1:WP_011611066.1 74 AYTGEISGLMLKDVGVSYVIVGHSERRQYFGETDETVNMRLKAAQKHGLTPILCVGETKQQRDSGETES 142 ***************************************************************999999 PP TIGR00419 137 nvattaaaaA....lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasv 201 + + a e+ v+A+EP+++iGtG + ea+ v + +r k + +v ++yG+sv lcl|NCBI__GCF_000014265.1:WP_011611066.1 143 HIFSQLANDLvdvdQENLVIAYEPIWAIGTGDTCEAKEANRVIGLIR------GKLNNSNVTIQYGGSV 205 998877654445558999*****************************......5556889********* PP TIGR00419 202 taaedaelaaqldvdGvLlasavlkae 228 + ++ + +aq ++dG+L+++a+l +e lcl|NCBI__GCF_000014265.1:WP_011611066.1 206 KPNNVDDIMAQEEIDGALVGGASLNPE 232 ***********************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (241 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: 5.69 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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