Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_029134995.1 A3GO_RS0120560 triose-phosphate isomerase
Query= BRENDA::P0A858 (255 letters) >NCBI__GCF_000428045.1:WP_029134995.1 Length = 250 Score = 266 bits (681), Expect = 2e-76 Identities = 130/249 (52%), Positives = 172/249 (69%) Query: 1 MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60 MR PLV GNWK+NGS + L+ ++ +A V VA+ P +Y+ +++ +G+ + Sbjct: 1 MRQPLVAGNWKMNGSLESIGLLLQGIKAGMADVRRAEVAVCAPAIYLPAVQQQLQGTAVA 60 Query: 61 LGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQG 120 GAQ+V SGA+TGE + +ML+D G +Y+I+GHSERR YH ESDEL+A+KFA + G Sbjct: 61 WGAQDVSAESSGAYTGEIATSMLQDFGCKYVIVGHSERRAYHAESDELVARKFAAARAAG 120 Query: 121 LTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSATP 180 L P+LC+GET AE E G TE V ARQ+DAV+ +G AA V+AYEPVWAIGTG++ATP Sbjct: 121 LVPILCVGETLAEREQGITESVVARQLDAVINLEGVAALADGVVAYEPVWAIGTGETATP 180 Query: 181 AQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKAD 240 QAQ VH FIR+ +A DA +A+ + I YGGS+ NA EL A+PDIDG L+GGASL A Sbjct: 181 DQAQEVHAFIRNRVAGHDAGVADGLRILYGGSMKPGNAQELIAKPDIDGGLIGGASLDAG 240 Query: 241 AFAVIVKAA 249 F I AA Sbjct: 241 DFLGICTAA 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: 186 Number of extensions: 6 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: 255 Length of database: 250 Length adjustment: 24 Effective length of query: 231 Effective length of database: 226 Effective search space: 52206 Effective search space used: 52206 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_029134995.1 A3GO_RS0120560 (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.aa/TIGR00419.hmm # target sequence database: /tmp/gapView.19144.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7e-77 244.3 1.4 8e-77 244.1 1.4 1.0 1 lcl|NCBI__GCF_000428045.1:WP_029134995.1 A3GO_RS0120560 triose-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000428045.1:WP_029134995.1 A3GO_RS0120560 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 244.1 1.4 8e-77 8e-77 1 227 [. 5 239 .. 5 240 .. 0.99 Alignments for each domain: == domain 1 score: 244.1 bits; conditional E-value: 8e-77 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGa 68 lv +n+K+n+s+++ l+++ +++ +a++ evav p ++l+ v+++++ + + +Aq+v a +sGa lcl|NCBI__GCF_000428045.1:WP_029134995.1 5 LVAGNWKMNGSLESIGLLLQGIKAGMADVRRAEVAVCAPAIYLPAVQQQLQgTAVAWGAQDVSAESSGA 73 799************************************************999*************** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere....... 130 +tGei ml+d+G+k+v++gHsErR++++e+del++ k+a +++ gl +++Cvgetl+ere lcl|NCBI__GCF_000428045.1:WP_029134995.1 74 YTGEIATSMLQDFGCKYVIVGHSERRAYHAESDELVARKFAAARAAGLVPILCVGETLAEREqgitesv 142 ********************************************************************9 PP TIGR00419 131 aartinnvattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGa 199 +ar++++v + +++aAl + vvA+EPv++iGtG ++++ +a++v++++r+ ++ ++ va+ r+lyG+ lcl|NCBI__GCF_000428045.1:WP_029134995.1 143 VARQLDAVINLEGVAALADGVVAYEPVWAIGTGETATPDQAQEVHAFIRNRVAGHDAGVADGLRILYGG 211 9******************************************************************** PP TIGR00419 200 svtaaedaelaaqldvdGvLlasavlka 227 s++ ++++el+a++d+dG L+++a+l a lcl|NCBI__GCF_000428045.1:WP_029134995.1 212 SMKPGNAQELIAKPDIDGGLIGGASLDA 239 *************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (250 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.27 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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