Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_050656343.1 C1M55_RS15105 triose-phosphate isomerase
Query= BRENDA::P9WG43 (261 letters) >NCBI__GCF_002893965.1:WP_050656343.1 Length = 261 Score = 398 bits (1023), Expect = e-116 Identities = 196/261 (75%), Positives = 226/261 (86%) Query: 1 MSRKPLIAGNWKMNLNHYEAIALVQKIAFSLPDKYYDRVDVAVIPPFTDLRSVQTLVDGD 60 M RKPLIAGNWKMNLNH EAIALVQKIAFSLP KY+D+VDV VIPPFTD+RSVQTL++GD Sbjct: 1 MVRKPLIAGNWKMNLNHLEAIALVQKIAFSLPAKYFDKVDVTVIPPFTDIRSVQTLIEGD 60 Query: 61 KLRLTYGAQDLSPHDSGAYTGDVSGAFLAKLGCSYVVVGHSERRTYHNEDDALVAAKAAT 120 KL LTYGAQD+S HDSGA+TG++SG+ LAKLGC++VVVGHSERRT H E + V AK Sbjct: 61 KLLLTYGAQDVSAHDSGAFTGEISGSMLAKLGCTFVVVGHSERRTLHGETNETVLAKTKA 120 Query: 121 ALKHGLTPIVCIGEHLDVREAGNHVAHNIEQLRGSLAGLLAEQIGSVVIAYEPVWAIGTG 180 ALK+GLTPIVCIGE L++REAG HVA+N++QL+GSLAGL AE+I +VIAYEPVWAIGTG Sbjct: 121 ALKNGLTPIVCIGEGLEIREAGEHVAYNVDQLKGSLAGLSAEEISKIVIAYEPVWAIGTG 180 Query: 181 RVASAADAQEVCAAIRKELASLASPRIADTVRVLYGGSVNAKNVGDIVAQDDVDGGLVGG 240 RVASAADAQEVCAA+R +A LA +A VRVLYGGSV++KNVG+IV Q DVDG LVGG Sbjct: 181 RVASAADAQEVCAAVRATVAELADAEVAAGVRVLYGGSVSSKNVGEIVGQADVDGALVGG 240 Query: 241 ASLDGEHFATLAAIAAGGPLP 261 ASL + FATL+AIAAGGPLP Sbjct: 241 ASLKADEFATLSAIAAGGPLP 261 Lambda K H 0.318 0.135 0.393 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: 284 Number of extensions: 5 Number of successful extensions: 1 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: 261 Length of database: 261 Length adjustment: 25 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 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 WP_050656343.1 C1M55_RS15105 (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.2004555.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-61 194.4 4.0 1.4e-61 194.2 4.0 1.0 1 NCBI__GCF_002893965.1:WP_050656343.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002893965.1:WP_050656343.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 194.2 4.0 1.4e-61 1.4e-61 1 228 [] 6 246 .. 6 246 .. 0.94 Alignments for each domain: == domain 1 score: 194.2 bits; conditional E-value: 1.4e-61 TIGR00419 1 lviinfKlnesvgkvelevaklaeevase..agvevavappfvdldvvkdeve.se..iqvaAqnvdavksGa 68 l+ +n+K+n + +v+k+a + + ++v v+v ppf d++ v+ +e + ++ +Aq+v a++sGa NCBI__GCF_002893965.1:WP_050656343.1 6 LIAGNWKMNLNHLEAIALVQKIAFSLPAKyfDKVDVTVIPPFTDIRSVQTLIEgDKllLTYGAQDVSAHDSGA 78 689********99**********98876534799****************999544225668*********** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartin.nvat 140 ftGeis ml+ lG+ +v++gHsErR+l+ e++e + +k + + gl+++vC+ge le rea++++ nv + NCBI__GCF_002893965.1:WP_050656343.1 79 FTGEISGSMLAKLGCTFVVVGHSERRTLHGETNETVLAKTKAALKNGLTPIVCIGEGLEIREAGEHVAyNVDQ 151 **************************************************************99987438999 PP TIGR00419 141 taaaaA......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaed 206 ++ A +++ v+A+EPv++iGtG+++s A+a++v + vr +++ +++eva vrvlyG+sv++++ NCBI__GCF_002893965.1:WP_050656343.1 152 LKGSLAglsaeeISKIVIAYEPVWAIGTGRVASAADAQEVCAAVRATVAElADAEVAAGVRVLYGGSVSSKNV 224 99999999999999***********************************99********************** PP TIGR00419 207 aelaaqldvdGvLlasavlkae 228 e + q dvdG+L+++a+lka+ NCBI__GCF_002893965.1:WP_050656343.1 225 GEIVGQADVDGALVGGASLKAD 246 ********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (261 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: 10.77 // [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