Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate GFF4691 PS417_24000 triosephosphate isomerase
Query= BRENDA::P0A858 (255 letters) >FitnessBrowser__WCS417:GFF4691 Length = 251 Score = 234 bits (598), Expect = 1e-66 Identities = 125/250 (50%), Positives = 165/250 (66%), Gaps = 2/250 (0%) Query: 1 MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60 MR +V GNWK++G+R V EL++ LR LA +G VA+ PP ++I+ +G I Sbjct: 1 MRRTMVAGNWKMHGTRASVAELINGLR-HLALPSGVDVAVFPPCLHINQVVDGLKGKSIQ 59 Query: 61 LGAQNVDLN-LSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQ 119 +GAQN + + GA TGE S + L D G Y+++GHSERR E D + +KFA + Sbjct: 60 VGAQNSAVEPMQGALTGEISPSQLVDAGCSYVLVGHSERRQMMGERDGTLNRKFAAAQAC 119 Query: 120 GLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSAT 179 GL PVLCIGET + E+GKT EV +RQ+ ++++ G AF AVIAYEPVWAIGTG +AT Sbjct: 120 GLIPVLCIGETLEQRESGKTLEVVSRQLGSIIEELGVGAFAKAVIAYEPVWAIGTGLTAT 179 Query: 180 PAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKA 239 P QAQ VH IR +A ++ +A+ V + YGGSV A+NA ELF PDIDG L+GGASL A Sbjct: 180 PQQAQDVHAAIRAQLAAENSEVAQGVRLLYGGSVKAANAVELFGMPDIDGGLIGGASLNA 239 Query: 240 DAFAVIVKAA 249 D F I +AA Sbjct: 240 DEFGAICRAA 249 Lambda K H 0.316 0.130 0.366 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: 177 Number of extensions: 7 Number of successful extensions: 3 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: 255 Length of database: 251 Length adjustment: 24 Effective length of query: 231 Effective length of database: 227 Effective search space: 52437 Effective search space used: 52437 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 GFF4691 PS417_24000 (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.28246.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-68 217.0 0.5 1.8e-68 216.8 0.5 1.0 1 lcl|FitnessBrowser__WCS417:GFF4691 PS417_24000 triosephosphate isom Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF4691 PS417_24000 triosephosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 216.8 0.5 1.8e-68 1.8e-68 1 228 [] 5 240 .. 5 240 .. 0.95 Alignments for each domain: == domain 1 score: 216.8 bits; conditional E-value: 1.8e-68 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdav.ksGaftGei 73 +v +n+K+++++ +v+++++ l+ ++a ++gv vav pp ++++ v+d ++ iqv+Aqn + +Ga tGei lcl|FitnessBrowser__WCS417:GFF4691 5 MVAGNWKMHGTRASVAELINGLR-HLALPSGVDVAVFPPCLHINQVVDGLKgKSIQVGAQNSAVEpMQGALTGEI 78 699******************98.69*************************999*******9987368******* PP TIGR00419 74 sAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaaaA.. 146 s l+d+G+ +vl+gHsErR ++ e d ++ k+a +++ gl +v+C+getle+re+++t+++v ++ + + lcl|FitnessBrowser__WCS417:GFF4691 79 SPSQLVDAGCSYVLVGHSERRQMMGERDGTLNRKFAAAQACGLIPVLCIGETLEQRESGKTLEVVSRQLGSIIee 153 *********************************************************888888887777666555 PP TIGR00419 147 .....lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvd 216 + ++v+A+EPv++iGtG ++++ +a+ v++ +r l+ + eva+ vr+lyG+sv+aa+++el+ +d+d lcl|FitnessBrowser__WCS417:GFF4691 154 lgvgaFAKAVIAYEPVWAIGTGLTATPQQAQDVHAAIRAQLAAENSEVAQGVRLLYGGSVKAANAVELFGMPDID 228 55555********************************************************************** PP TIGR00419 217 GvLlasavlkae 228 G L+++a+l a+ lcl|FitnessBrowser__WCS417:GFF4691 229 GGLIGGASLNAD 240 *********997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (251 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: 6.64 // [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