Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_029933953.1 N746_RS0103365 triose-phosphate isomerase
Query= BRENDA::P0A858 (255 letters) >NCBI__GCF_000711195.1:WP_029933953.1 Length = 256 Score = 254 bits (650), Expect = 9e-73 Identities = 129/250 (51%), Positives = 169/250 (67%), Gaps = 1/250 (0%) Query: 1 MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60 MR P V GNWK++GS+ M+ L++ L + + +A+ PP +YID K+ + I Sbjct: 1 MRRPFVAGNWKMHGSKAMIQTLLAELVEGAKPLESVDMAVCPPSVYIDYVKQGLVETKIS 60 Query: 61 LGAQNV-DLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQ 119 +G QN+ D+ GAFTGE + MLKD+G Y+I+GHSERRT + E+DE +A K ++ + Sbjct: 61 VGGQNMADVAEQGAFTGEVTGVMLKDVGCDYVIVGHSERRTLYAETDEQVANKVSIALAE 120 Query: 120 GLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSAT 179 GLTP+LC+GET E E+ TE+V Q+ AVL G AF V+AYEPVWAIGTG +A+ Sbjct: 121 GLTPILCVGETLKERESNVTEKVVGSQMQAVLDKVGVKAFAKVVVAYEPVWAIGTGMTAS 180 Query: 180 PAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKA 239 P QAQ VH FIR +AK DA IAE +IIQYGGSV +NA ELF+Q DIDG L+GGASL A Sbjct: 181 PQQAQDVHAFIRGLVAKQDATIAESLIIQYGGSVKPNNAKELFSQTDIDGGLIGGASLNA 240 Query: 240 DAFAVIVKAA 249 F I +AA Sbjct: 241 VDFLAICEAA 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: 190 Number of extensions: 6 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: 256 Length adjustment: 24 Effective length of query: 231 Effective length of database: 232 Effective search space: 53592 Effective search space used: 53592 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: 47 (22.7 bits)
Align candidate WP_029933953.1 N746_RS0103365 (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.3905.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.9e-74 234.5 4.5 7.9e-74 234.3 4.5 1.0 1 lcl|NCBI__GCF_000711195.1:WP_029933953.1 N746_RS0103365 triose-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000711195.1:WP_029933953.1 N746_RS0103365 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 234.3 4.5 7.9e-74 7.9e-74 1 227 [. 5 240 .. 5 241 .. 0.98 Alignments for each domain: == domain 1 score: 234.3 bits; conditional E-value: 7.9e-74 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnv.davksG 67 +v +n+K+++s + ++++a+l e + v +av pp v++d vk+ + ++i+v+ qn+ d+ ++G lcl|NCBI__GCF_000711195.1:WP_029933953.1 5 FVAGNWKMHGSKAMIQTLLAELVEGAKPLESVDMAVCPPSVYIDYVKQGLVeTKISVGGQNMaDVAEQG 73 699********************************************98544*********757899** PP TIGR00419 68 aftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleere...... 130 aftGe++ mlkd+G+ +v++gHsErR+l +e+de +++kv+ + + gl++++Cvgetl+ere lcl|NCBI__GCF_000711195.1:WP_029933953.1 74 AFTGEVTGVMLKDVGCDYVIVGHSERRTLYAETDEQVANKVSIALAEGLTPILCVGETLKEREsnvtek 142 ********************************************************************* PP TIGR00419 131 .aartinnvattaaaaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyG 198 +++++++v+++ ++ A+ ++vvA+EPv++iGtG+++s+ +a+ v++++r ++k ++ +aes +++yG lcl|NCBI__GCF_000711195.1:WP_029933953.1 143 vVGSQMQAVLDKVGVKAFAKVVVAYEPVWAIGTGMTASPQQAQDVHAFIRGLVAKQDATIAESLIIQYG 211 99******************************************************************* PP TIGR00419 199 asvtaaedaelaaqldvdGvLlasavlka 227 +sv+ ++++el+ q d+dG L+++a+l a lcl|NCBI__GCF_000711195.1:WP_029933953.1 212 GSVKPNNAKELFSQTDIDGGLIGGASLNA 240 **************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (256 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: 10.69 // [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