Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_035239783.1 Q366_RS13325 triose-phosphate isomerase
Query= SwissProt::Q8XKU1 (248 letters) >NCBI__GCF_000745975.1:WP_035239783.1 Length = 255 Score = 218 bits (554), Expect = 1e-61 Identities = 111/249 (44%), Positives = 162/249 (65%), Gaps = 2/249 (0%) Query: 2 RTPIIAGNWKMHYTIDEAVKLVEELKPLVKDAK-CEVVVCPTFVCLDAVKKAV-EGTNIK 59 RTP+IAGNWKM+ T +AV ++L L K ++++ PT + L V A+ + + ++ Sbjct: 7 RTPLIAGNWKMYKTGTQAVAAAKQLADLTKGVDGVDIMIAPTALSLPLVAAALGKDSQVR 66 Query: 60 VGAQNMHFEEKGAFTGEIAPRMLEAMNIDYVIIGHSERREYFNETDETCNKKVKAAFAHN 119 +GAQN++ +GAFTGE++ +M++ DYVIIGHSERR+YF ETDE+ K++AA Sbjct: 67 LGAQNIYPGTEGAFTGEVSGQMIKDAGADYVIIGHSERRQYFGETDESVGHKIRAALDAG 126 Query: 120 LTPILCCGETLEQRENGTTNDVIKAQITADLEGLTKEQAEKVVIAYEPIWAIGTGKTATS 179 L P++C GET QRE T V+ QI+ L+G E+ + +++AYEP+WAIGTGKTA Sbjct: 127 LIPVMCIGETERQREADKTFFVLDKQISDGLKGFDLEELDSLILAYEPVWAIGTGKTAGP 186 Query: 180 DQANETIAAIRAMVAEMFGQEVADKVRIQYGGSVKPNTIAEQMAKSDIDGALVGGASLVA 239 +Q E +R ++ + + +A K RI YGGSVKP I + M D+DGALVGGASL Sbjct: 187 EQVKEVHGFLRHLLRGKYSESLAAKTRILYGGSVKPGNIKDLMQLEDVDGALVGGASLNP 246 Query: 240 ADFAQIVNY 248 DF +I+ + Sbjct: 247 EDFNKIIRF 255 Lambda K H 0.316 0.131 0.376 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: 152 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: 248 Length of database: 255 Length adjustment: 24 Effective length of query: 224 Effective length of database: 231 Effective search space: 51744 Effective search space used: 51744 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_035239783.1 Q366_RS13325 (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.23712.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-60 190.7 0.0 2e-60 190.5 0.0 1.0 1 lcl|NCBI__GCF_000745975.1:WP_035239783.1 Q366_RS13325 triose-phosphate is Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745975.1:WP_035239783.1 Q366_RS13325 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 190.5 0.0 2e-60 2e-60 1 228 [] 10 247 .. 10 247 .. 0.91 Alignments for each domain: == domain 1 score: 190.5 bits; conditional E-value: 2e-60 TIGR00419 1 lviinfK.lnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve..seiqvaAqnvdavks 66 l+ +n+K ++ +++ v +la+ +++gv + +ap + l+ v+ ++ s+++++Aqn+ + lcl|NCBI__GCF_000745975.1:WP_035239783.1 10 LIAGNWKmYKTGTQAV-AAAKQLADLTKGVDGVDIMIAPTALSLPLVAAALGkdSQVRLGAQNIYPGTE 77 689****666665555.4567788888899*******************9976799************* PP TIGR00419 67 GaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaarti 135 GaftGe+s +m+kd+Ga +v+igHsErR ++ e+de +++k+ + + gl +v+C+get+ +rea +t+ lcl|NCBI__GCF_000745975.1:WP_035239783.1 78 GAFTGEVSGQMIKDAGADYVIIGHSERRQYFGETDESVGHKIRAALDAGLIPVMCIGETERQREADKTF 146 ****************************************************************99998 PP TIGR00419 136 nnvattaaaaA.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvl 196 ++ ++ + l++ ++A+EPv++iGtGk++ + + ++v++++r l+ s+ +a ++r+l lcl|NCBI__GCF_000745975.1:WP_035239783.1 147 FVLDKQISDGLkgfdleeLDSLILAYEPVWAIGTGKTAGPEQVKEVHGFLRHLLRGkYSESLAAKTRIL 215 7777765544356777779999*****************************777656999********* PP TIGR00419 197 yGasvtaaedaelaaqldvdGvLlasavlkae 228 yG+sv+ ++ ++l+ dvdG+L+++a+l +e lcl|NCBI__GCF_000745975.1:WP_035239783.1 216 YGGSVKPGNIKDLMQLEDVDGALVGGASLNPE 247 ***************9************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (255 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: 8.60 // [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