Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_013819888.1 METME_RS16495 triose-phosphate isomerase
Query= SwissProt::P50921 (256 letters) >NCBI__GCF_000214665.1:WP_013819888.1 Length = 248 Score = 231 bits (589), Expect = 1e-65 Identities = 123/251 (49%), Positives = 163/251 (64%), Gaps = 11/251 (4%) Query: 1 MRHPVVMGNWKLNGSKEMVVDLL----NGLNAELEGVTGVDVAVAPPALFVDLAERTLTE 56 MR P++MGNWK+NGS+E V L +GLNA + +VAV P ++V L Sbjct: 1 MRQPLIMGNWKMNGSREEGVQLAKALADGLNAGSQ-----EVAVCVPFVYVSDIRGAL-- 53 Query: 57 AGSAIILGAQNTDLNNSGAFTGDMSPAMLKEFGATHIIIGHSERREYHAESDEFVAKKFA 116 A S I LGAQN SGA+TG++S AML + G + ++GHSERR Y+ ++ + VA +F Sbjct: 54 ASSPIALGAQNVADQASGAYTGEISAAMLADCGVKYALVGHSERRSYYGDTSQSVANRFC 113 Query: 117 FLKENGLTPVLCIGESDAQNEAGETMAVCARQLDAVINTQGVEALEGAIIAYEPIWAIGT 176 ++ + PVLC+GE+ + E T V QLDAVI+ G+EA A+IAYEP+WAIGT Sbjct: 114 QAQKQNVIPVLCVGETLEEREQDRTFQVVDEQLDAVIDAAGIEAFANAVIAYEPVWAIGT 173 Query: 177 GKAATAEDAQRIHAQIRAHIAEKSEAVAKNVVIQYGGSVKPENAAAYFAQPDIDGALVGG 236 GK A+ E AQ +H IR IA+++ A+A+ V I YGGSVKP+NA FA PDIDG LVGG Sbjct: 174 GKTASDEQAQEVHQYIRKRIADRNPAIAEKVQILYGGSVKPDNAKGLFAMPDIDGGLVGG 233 Query: 237 AALDAKSFAAI 247 A+LDAK F I Sbjct: 234 ASLDAKGFLQI 244 Lambda K H 0.314 0.130 0.364 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: 166 Number of extensions: 4 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: 256 Length of database: 248 Length adjustment: 24 Effective length of query: 232 Effective length of database: 224 Effective search space: 51968 Effective search space used: 51968 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 (21.5 bits) S2: 46 (22.3 bits)
Align candidate WP_013819888.1 METME_RS16495 (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.9254.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-71 226.1 0.9 2.8e-71 226.0 0.9 1.0 1 lcl|NCBI__GCF_000214665.1:WP_013819888.1 METME_RS16495 triose-phosphate i Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000214665.1:WP_013819888.1 METME_RS16495 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 226.0 0.9 2.8e-71 2.8e-71 1 227 [. 5 238 .. 5 239 .. 0.95 Alignments for each domain: == domain 1 score: 226.0 bits; conditional E-value: 2.8e-71 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGa 68 l+++n+K+n+s+++ ++ la+ + evav +pfv+++ ++ ++ s i ++Aqnv + sGa lcl|NCBI__GCF_000214665.1:WP_013819888.1 5 LIMGNWKMNGSREEGVQLAKALADGLN-AGSQEVAVCVPFVYVSDIRGALAsSPIALGAQNVADQASGA 72 79**********998887777877775.45679***************998799*************** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere....... 130 +tGeisA+ml+d+G+k+ l+gHsErRs+ +++ +++++ +++++++ +v+Cvgetleere lcl|NCBI__GCF_000214665.1:WP_013819888.1 73 YTGEISAAMLADCGVKYALVGHSERRSYYGDTSQSVANRFCQAQKQNVIPVLCVGETLEEREqdrtfqv 141 **************************************************************8888888 PP TIGR00419 131 aartinnvattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGa 199 + +++++v + a++ A+ ++v+A+EPv++iGtGk++s +a++v++ +r ++ ++ +ae+v++lyG+ lcl|NCBI__GCF_000214665.1:WP_013819888.1 142 VDEQLDAVIDAAGIEAFANAVIAYEPVWAIGTGKTASDEQAQEVHQYIRKRIADRNPAIAEKVQILYGG 210 7888888888889999***************************************************** PP TIGR00419 200 svtaaedaelaaqldvdGvLlasavlka 227 sv+ +++ l+a +d+dG L+++a+l a lcl|NCBI__GCF_000214665.1:WP_013819888.1 211 SVKPDNAKGLFAMPDIDGGLVGGASLDA 238 *************************988 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (248 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: 8.90 // [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