Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate Synpcc7942_1261 Synpcc7942_1261 triosephosphate isomerase
Query= SwissProt::P00943 (253 letters) >FitnessBrowser__SynE:Synpcc7942_1261 Length = 263 Score = 240 bits (612), Expect = 2e-68 Identities = 127/248 (51%), Positives = 173/248 (69%), Gaps = 11/248 (4%) Query: 1 MRKPIIAGNWKMHKTLAEAVQFVEDVKGHVPPADEVISVV-CAPFLFLDRLVQAADGTDL 59 +R+ IIAGNWKM+KT AEA++F++ + E VV CAPF L L + G+ + Sbjct: 22 VRRIIIAGNWKMYKTQAEALEFLQAFLPQLSETPESRKVVLCAPFTTLSSLSKTLHGSRV 81 Query: 60 KIGAQTMHFADQGAYTGEVSPVMLKDLGVTYVILGHSERRQMFAETDETVNKKVLAAFTR 119 ++GAQ +H+A +GA+TGE+S ML ++GV YV++GHSERRQ F ETDETVN+++LAA + Sbjct: 82 RVGAQNIHWAKEGAFTGEISGAMLTEIGVRYVVVGHSERRQYFGETDETVNQRLLAAQSF 141 Query: 120 GLIPIICCGESLEEREAGQTNAVVASQVEKALAGLTPEQVKQAVIAYEPIWAIGTGKSST 179 GL+PI+C GES ++R+AG+T AV++ Q+E+ L G + VIAYEPIWAIGTG + Sbjct: 142 GLLPILCVGESKQQRDAGETEAVISRQLERGLVGADQTNL---VIAYEPIWAIGTGDTCA 198 Query: 180 PEDANSVCGHIRSVVSRLFGPEAAEAIRIQYGGSVKPDNIRDFLAQQQIDGPLVGGASLE 239 E+AN V G IRS + P IQYGGSVKP+NI + +AQ +IDG LVGGASLE Sbjct: 199 AEEANRVIGLIRSQLKDTDVP-------IQYGGSVKPENIDEIMAQPEIDGALVGGASLE 251 Query: 240 PASFLQLV 247 SF ++V Sbjct: 252 AESFARIV 259 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: 212 Number of extensions: 11 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: 263 Length adjustment: 24 Effective length of query: 229 Effective length of database: 239 Effective search space: 54731 Effective search space used: 54731 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: 47 (22.7 bits)
Align candidate Synpcc7942_1261 Synpcc7942_1261 (triosephosphate 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.7750.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-54 169.4 0.0 6.6e-54 169.1 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_1261 Synpcc7942_1261 triosephosphate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_1261 Synpcc7942_1261 triosephosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 169.1 0.0 6.6e-54 6.6e-54 1 228 [] 26 253 .. 26 253 .. 0.92 Alignments for each domain: == domain 1 score: 169.1 bits; conditional E-value: 6.6e-54 TIGR00419 1 lviinfKlnesvgkvelevaklaeevase.agvevavappfvdldvvkdeve.seiqvaAqnvdavksG 67 ++ +n+K+ + + + ++ +++++ + +v++ pf l+ +++ ++ s+++v+Aqn++ k G lcl|FitnessBrowser__SynE:Synpcc7942_1261 26 IIAGNWKMYKTQAEALEFLQAFLPQLSETpESRKVVLCAPFTTLSSLSKTLHgSRVRVGAQNIHWAKEG 94 6899***888999999999999999998626789******************9**************** PP TIGR00419 68 aftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartin 136 aftGeis +ml ++G+++v++gHsErR ++ e+de +++++ ++ gl +++Cvge++++r+a++t lcl|FitnessBrowser__SynE:Synpcc7942_1261 95 AFTGEISGAMLTEIGVRYVVVGHSERRQYFGETDETVNQRLLAAQSFGLLPILCVGESKQQRDAGETEA 163 *****************************************************************9988 PP TIGR00419 137 nvattaaaaA....lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasv 201 ++ ++ + ++ v+A+EP+++iGtG + + ea+ v + +r lk +v ++yG+sv lcl|FitnessBrowser__SynE:Synpcc7942_1261 164 VISRQLERGLvgadQTNLVIAYEPIWAIGTGDTCAAEEANRVIGLIRSQLK------DTDVPIQYGGSV 226 888775432222358999*****************************4444......5799******** PP TIGR00419 202 taaedaelaaqldvdGvLlasavlkae 228 + ++ e +aq+++dG+L+++a+l ae lcl|FitnessBrowser__SynE:Synpcc7942_1261 227 KPENIDEIMAQPEIDGALVGGASLEAE 253 ************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (263 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: 10.89 // [ok]
This GapMind analysis is from Sep 17 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