Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_008991764.1 I215_RS09580 triose-phosphate isomerase
Query= BRENDA::Q10657 (247 letters) >NCBI__GCF_000300875.1:WP_008991764.1 Length = 249 Score = 219 bits (559), Expect = 3e-62 Identities = 119/247 (48%), Positives = 162/247 (65%), Gaps = 4/247 (1%) Query: 3 RKFFVGGNWKMNGDYASVDGIVTFLNASADNSSVDVVVAPPAPYLAYAKSKLK-AGVLVA 61 R+ V GNWKMN D A +++ L N+ V V +AP L A LK V V Sbjct: 2 REKIVAGNWKMNNDLAETQALISDLRKVLTNTDVKVKIAPTYVNLYPAYETLKDTAVEVV 61 Query: 62 AQNCYKVPKGAFTGEISPAMIKDLGLEWVILGHSERRHVFGESDALIAEKTVHALEAGIK 121 AQN ++ GA+TGE+S M+K +G++ VILGHSERR FGE DAL+A+K A++AG+ Sbjct: 62 AQNMHQAKSGAYTGEVSADMLKSIGIQTVILGHSERRAYFGEDDALLAQKVSAAVDAGLN 121 Query: 122 VVFCIGEKLEEREAGHTKDVNFRQLQAIVDK--GVSWENIVIAYEPVWAIGTGKTASGEQ 179 V+FC GE+LE+R++ D+ QL++ + +W+ IV+AYEPVWAIGTG+TAS EQ Sbjct: 122 VIFCFGEELEDRKSDKHFDLVASQLKSGLFHLPASAWKQIVLAYEPVWAIGTGETASPEQ 181 Query: 180 AQEVHEWIRAFLKEKVSPAVADATRIIYGGSVTADNAAELGKKPDIDGFLVGGASLK-PD 238 AQE+HE+IR + + ++AD I+YGGSV NA E+ KPD+DG L+GGASL D Sbjct: 182 AQEMHEFIRKTVAGQYDASLADGVSILYGGSVKPANATEIFSKPDVDGGLIGGASLNAED 241 Query: 239 FVKIINA 245 FV I+NA Sbjct: 242 FVAIVNA 248 Lambda K H 0.317 0.134 0.396 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: 180 Number of extensions: 8 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: 247 Length of database: 249 Length adjustment: 24 Effective length of query: 223 Effective length of database: 225 Effective search space: 50175 Effective search space used: 50175 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_008991764.1 I215_RS09580 (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.524900.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-66 210.3 0.1 2e-66 210.1 0.1 1.0 1 NCBI__GCF_000300875.1:WP_008991764.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000300875.1:WP_008991764.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 210.1 0.1 2e-66 2e-66 1 228 [] 5 240 .. 5 240 .. 0.93 Alignments for each domain: == domain 1 score: 210.1 bits; conditional E-value: 2e-66 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftGe 72 +v +n+K+n+ + + + ++++l++ + +++v+v +ap +v l + + ++ + ++v+Aqn++ ksGa+tGe NCBI__GCF_000300875.1:WP_008991764.1 5 IVAGNWKMNNDLAETQALISDLRKVL-TNTDVKVKIAPTYVNLYPAYETLKdTAVEVVAQNMHQAKSGAYTGE 76 699*******************9766.56899******************9899******************* PP TIGR00419 73 isAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaa.. 143 +sA+mlk +G++ v++gHsErR+++ e d l+++kv+ + + gl+++ C ge le+r++ ++++ va + + NCBI__GCF_000300875.1:WP_008991764.1 77 VSADMLKSIGIQTVILGHSERRAYFGEDDALLAQKVSAAVDAGLNVIFCFGEELEDRKSDKHFDLVASQLKsg 149 **********************************************************777777777665522 PP TIGR00419 144 .....aaAlepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaedaela 210 a A+++ v+A+EPv++iGtG ++s+ +a+++++++r ++ ++ +a+ v++lyG+sv+ a+++e + NCBI__GCF_000300875.1:WP_008991764.1 150 lfhlpASAWKQIVLAYEPVWAIGTGETASPEQAQEMHEFIRKTVAGqYDASLADGVSILYGGSVKPANATEIF 222 33333788*********************************9999879************************* PP TIGR00419 211 aqldvdGvLlasavlkae 228 ++dvdG L+++a+l ae NCBI__GCF_000300875.1:WP_008991764.1 223 SKPDVDGGLIGGASLNAE 240 ***************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (249 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: 14.19 // [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