Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_057508448.1 ABB28_RS09765 triose-phosphate isomerase
Query= BRENDA::P0A858 (255 letters) >NCBI__GCF_001431535.1:WP_057508448.1 Length = 251 Score = 254 bits (650), Expect = 9e-73 Identities = 133/251 (52%), Positives = 167/251 (66%), Gaps = 1/251 (0%) Query: 1 MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60 MR +V GNWKL+G+R LV+++ A G + I PP Y+ + + + Sbjct: 1 MRRKIVAGNWKLHGTREFATTLVTDIANG-APEQGVELVILPPLPYLGELADDFADTAVS 59 Query: 61 LGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG 120 GAQ+V N GA+TGE SA+ML ++GA+Y ++GHSERR YH ES EL+A+KFA G Sbjct: 60 FGAQDVSSNEKGAYTGEVSASMLHEVGARYGLVGHSERRQYHHESSELVARKFAAALHAG 119 Query: 121 LTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATP 180 L PVLC+GET + EAG+TE V A Q+ VL G FE AV+AYEPVWAIGTG++A+ Sbjct: 120 LVPVLCVGETLEQREAGQTEAVIASQLAPVLALVGGQGFENAVVAYEPVWAIGTGRTASK 179 Query: 181 AQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKAD 240 QAQ VH FIR +AKVDA IA+ + I YGGSV NAAELFAQPD+DG LVGGASL A Sbjct: 180 EQAQQVHAFIRGEVAKVDARIADSLTILYGGSVKPDNAAELFAQPDVDGGLVGGASLVAA 239 Query: 241 AFAVIVKAAEA 251 F I +AA A Sbjct: 240 DFLAIAQAAAA 250 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: 198 Number of extensions: 8 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: 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 WP_057508448.1 ABB28_RS09765 (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.6563.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-73 231.5 0.3 6.9e-73 231.2 0.3 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057508448.1 ABB28_RS09765 triose-phosphate i Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057508448.1 ABB28_RS09765 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 231.2 0.3 6.9e-73 6.9e-73 1 227 [. 5 238 .. 5 239 .. 0.95 Alignments for each domain: == domain 1 score: 231.2 bits; conditional E-value: 6.9e-73 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGa 68 +v +n+Kl+++++ ++v+++a+ a e+gve+++ pp +l ++d+ + ++ +Aq+v +++Ga lcl|NCBI__GCF_001431535.1:WP_057508448.1 5 IVAGNWKLHGTREFATTLVTDIANG-APEQGVELVILPPLPYLGELADDFAdTAVSFGAQDVSSNEKGA 72 699*******************865.8899*************99999987699*************** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinn 137 +tGe+sA ml+++Ga++ l+gHsErR +++e++el++ k+a + + gl +v+Cvgetle+rea++t + lcl|NCBI__GCF_001431535.1:WP_057508448.1 73 YTGEVSASMLHEVGARYGLVGHSERRQYHHESSELVARKFAAALHAGLVPVLCVGETLEQREAGQTEAV 141 **************************************************************9998777 PP TIGR00419 138 vattaa.aaA......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGa 199 +a + a + A +e++vvA+EPv++iGtG+++sk +a++v++++r ++kv++ +a+s +lyG+ lcl|NCBI__GCF_001431535.1:WP_057508448.1 142 IASQLApVLAlvggqgFENAVVAYEPVWAIGTGRTASKEQAQQVHAFIRGEVAKVDARIADSLTILYGG 210 7777652445889999***************************************************** PP TIGR00419 200 svtaaedaelaaqldvdGvLlasavlka 227 sv+ ++ael+aq+dvdG L+++a+l a lcl|NCBI__GCF_001431535.1:WP_057508448.1 211 SVKPDNAAELFAQPDVDGGLVGGASLVA 238 *************************976 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.62 // [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