Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_010960015.1 MCA_RS03330 triose-phosphate isomerase
Query= SwissProt::P50921 (256 letters) >NCBI__GCF_000008325.1:WP_010960015.1 Length = 250 Score = 233 bits (595), Expect = 2e-66 Identities = 121/252 (48%), Positives = 167/252 (66%), Gaps = 3/252 (1%) Query: 1 MRHPVVMGNWKLNGSKEMVVDLLNGLNAELEGVTGVDVAVAPPALFVDLAERTLTEAGSA 60 MR P+V+GNWK+NG V LLN + A + G +V V P +++ A L G+ Sbjct: 1 MRRPLVVGNWKMNGRSASVARLLNDILAGI-GDCKAEVGVCVPFVYIPQASEILK--GTK 57 Query: 61 IILGAQNTDLNNSGAFTGDMSPAMLKEFGATHIIIGHSERREYHAESDEFVAKKFAFLKE 120 ++LGAQN +NSGAFTG++S ML+EFG I+GHSERR + ES+E VA ++ + Sbjct: 58 VMLGAQNVADHNSGAFTGEISAGMLREFGCELAIVGHSERRLLYGESNELVASRYEQAIQ 117 Query: 121 NGLTPVLCIGESDAQNEAGETMAVCARQLDAVINTQGVEALEGAIIAYEPIWAIGTGKAA 180 L P+LC+GE+ Q E G T+AV Q+D V GV++LE A+IAYEP+WA+GTG++A Sbjct: 118 GHLKPILCVGETLEQREQGRTLAVIGAQIDTVFEFAGVQSLEHAVIAYEPVWAVGTGRSA 177 Query: 181 TAEDAQRIHAQIRAHIAEKSEAVAKNVVIQYGGSVKPENAAAYFAQPDIDGALVGGAALD 240 T AQ +H IR+ IA + VA+ V I YGGSVKPEN+A FA PDIDG L+GGA+LD Sbjct: 178 TTGQAQEVHYHIRSLIARWNPEVAQAVQIIYGGSVKPENSAELFAMPDIDGGLIGGASLD 237 Query: 241 AKSFAAIAKAAA 252 A++F +I + + Sbjct: 238 ARAFLSICHSVS 249 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: 168 Number of extensions: 5 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: 250 Length adjustment: 24 Effective length of query: 232 Effective length of database: 226 Effective search space: 52432 Effective search space used: 52432 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_010960015.1 MCA_RS03330 (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.30848.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 0.2 2.9e-71 225.9 0.2 1.0 1 lcl|NCBI__GCF_000008325.1:WP_010960015.1 MCA_RS03330 triose-phosphate iso Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008325.1:WP_010960015.1 MCA_RS03330 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 225.9 0.2 2.9e-71 2.9e-71 1 227 [. 5 238 .. 5 239 .. 0.98 Alignments for each domain: == domain 1 score: 225.9 bits; conditional E-value: 2.9e-71 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGa 68 lv++n+K+n+ +v+ +++++ + + + ++ ev+v +pfv+++ +++ ++ ++++++Aqnv ++sGa lcl|NCBI__GCF_000008325.1:WP_010960015.1 5 LVVGNWKMNGRSASVARLLNDILAGIGD-CKAEVGVCVPFVYIPQASEILKgTKVMLGAQNVADHNSGA 72 79***********************976.789*******************99**************** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere....... 130 ftGeisA ml+++G++ ++gHsErR l e++el++ + ++ + lk+++Cvgetle+re lcl|NCBI__GCF_000008325.1:WP_010960015.1 73 FTGEISAGMLREFGCELAIVGHSERRLLYGESNELVASRYEQAIQGHLKPILCVGETLEQREqgrtlav 141 **************************************************************9999999 PP TIGR00419 131 aartinnvattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGa 199 + +i++v + a++ le +v+A+EPv+++GtG++++ +a++v+ +r +++ ++eva+ v+++yG+ lcl|NCBI__GCF_000008325.1:WP_010960015.1 142 IGAQIDTVFEFAGVQSLEHAVIAYEPVWAVGTGRSATTGQAQEVHYHIRSLIARWNPEVAQAVQIIYGG 210 999****************************************************************** PP TIGR00419 200 svtaaedaelaaqldvdGvLlasavlka 227 sv+ +++ael+a +d+dG L+++a+l a lcl|NCBI__GCF_000008325.1:WP_010960015.1 211 SVKPENSAELFAMPDIDGGLIGGASLDA 238 *************************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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.11 // [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