Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_076477793.1 BW971_RS06720 triose-phosphate isomerase
Query= BRENDA::P9WG43 (261 letters) >NCBI__GCF_900156495.1:WP_076477793.1 Length = 262 Score = 404 bits (1039), Expect = e-118 Identities = 199/260 (76%), Positives = 223/260 (85%) Query: 2 SRKPLIAGNWKMNLNHYEAIALVQKIAFSLPDKYYDRVDVAVIPPFTDLRSVQTLVDGDK 61 +R PLIAGNWKMNLNH EAIALVQKIAF+LP KY+D+VDV V+PPFTD+RSVQT+VDGDK Sbjct: 3 NRTPLIAGNWKMNLNHLEAIALVQKIAFALPAKYFDKVDVTVLPPFTDIRSVQTVVDGDK 62 Query: 62 LRLTYGAQDLSPHDSGAYTGDVSGAFLAKLGCSYVVVGHSERRTYHNEDDALVAAKAATA 121 L LTYGAQDLS HDSGAYTGD+SGAFLAKLGCSYVVVGHSERRT H E D +VAAKA A Sbjct: 63 LLLTYGAQDLSQHDSGAYTGDISGAFLAKLGCSYVVVGHSERRTLHGETDEIVAAKAKAA 122 Query: 122 LKHGLTPIVCIGEHLDVREAGNHVAHNIEQLRGSLAGLLAEQIGSVVIAYEPVWAIGTGR 181 + HG+ PIVCIGE L+VREAG HVAH + Q++GSLAGL AEQIG V+AYEPVWAIGTGR Sbjct: 123 IDHGIVPIVCIGEPLEVREAGEHVAHCVAQVKGSLAGLSAEQIGRTVLAYEPVWAIGTGR 182 Query: 182 VASAADAQEVCAAIRKELASLASPRIADTVRVLYGGSVNAKNVGDIVAQDDVDGGLVGGA 241 VASA DAQEVCAA+R +A LA +AD VRVLYGGSV +KNVG++V + DVDG LVGGA Sbjct: 183 VASADDAQEVCAAVRDAIAQLADQAVADEVRVLYGGSVGSKNVGELVGKPDVDGALVGGA 242 Query: 242 SLDGEHFATLAAIAAGGPLP 261 SL + FATL AIAAGGPLP Sbjct: 243 SLKSDEFATLCAIAAGGPLP 262 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: 300 Number of extensions: 7 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: 262 Length adjustment: 25 Effective length of query: 236 Effective length of database: 237 Effective search space: 55932 Effective search space used: 55932 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_076477793.1 BW971_RS06720 (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.793203.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-59 187.9 1.7 1.4e-59 187.7 1.7 1.0 1 NCBI__GCF_900156495.1:WP_076477793.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900156495.1:WP_076477793.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 187.7 1.7 1.4e-59 1.4e-59 1 228 [] 7 247 .. 7 247 .. 0.93 Alignments for each domain: == domain 1 score: 187.7 bits; conditional E-value: 1.4e-59 TIGR00419 1 lviinfKlnesvgkvelevaklaeevase..agvevavappfvdldvvkdeve.se..iqvaAqnvdavksGa 68 l+ +n+K+n + +v+k+a + + ++v v+v ppf d++ v+ v+ + ++ +Aq++ ++sGa NCBI__GCF_900156495.1:WP_076477793.1 7 LIAGNWKMNLNHLEAIALVQKIAFALPAKyfDKVDVTVLPPFTDIRSVQTVVDgDKllLTYGAQDLSQHDSGA 79 689********99**********98866534799**************99999544225668*********** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaarti.nnvat 140 +tG+is + l+ lG+ +v++gHsErR+l+ e+de++++k + + g+ ++vC+ge le rea++++ va+ NCBI__GCF_900156495.1:WP_076477793.1 80 YTGDISGAFLAKLGCSYVVVGHSERRTLHGETDEIVAAKAKAAIDHGIVPIVCIGEPLEVREAGEHVaHCVAQ 152 **************************************************************99987356888 PP TIGR00419 141 taaaaA......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaed 206 ++ A + v+A+EPv++iGtG+++s +a++v + vrd +++ +++ va++vrvlyG+sv +++ NCBI__GCF_900156495.1:WP_076477793.1 153 VKGSLAglsaeqIGRTVLAYEPVWAIGTGRVASADDAQEVCAAVRDAIAQlADQAVADEVRVLYGGSVGSKNV 225 888888988898999***********************************9********************** PP TIGR00419 207 aelaaqldvdGvLlasavlkae 228 el+ ++dvdG+L+++a+lk++ NCBI__GCF_900156495.1:WP_076477793.1 226 GELVGKPDVDGALVGGASLKSD 247 ********************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (262 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 12.79 // [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