Align triosephosphate isomerase subunit (EC 5.3.1.1) (characterized)
to candidate WP_009140074.1 HMPREF9452_RS00185 triose-phosphate isomerase
Query= metacyc::MONOMER-13051 (252 letters) >NCBI__GCF_000225705.1:WP_009140074.1 Length = 257 Score = 266 bits (681), Expect = 2e-76 Identities = 130/248 (52%), Positives = 170/248 (68%), Gaps = 1/248 (0%) Query: 2 SRTPIIAGNWKLNMNPKETVEFVNAVKDQLPDPSK-VESVICAPAVDLDALLKAAEGSNL 60 +RT +IAGNWK+N + + + + L VE ++C P +DL + +GS + Sbjct: 5 NRTLLIAGNWKMNNDVQAAATLADELVAALDGVDNGVEVLVCPPTIDLTTVAAKLDGSAI 64 Query: 61 HVGAENCYWENSGAFTGETSPAVLKEMGVQYVIIGHSERRDYFHETDEDINKKAKAIFAN 120 +GA+N YWE +GA+TGE+S +LK G Y IIGHSERRDYFHETDED NKKAKA+ A Sbjct: 65 KLGAQNVYWEAAGAYTGESSCDMLKSAGCTYCIIGHSERRDYFHETDEDQNKKAKALVAA 124 Query: 121 GLTPILCCGESLETREAGKENEWVVSQIKAGLEGLTSEQVSKLVIAYEPIWAIGTGKTAS 180 GL P+ CCGE LE REAG E VV+Q+KAGLEGL ++LV+AYEPIWAIGTG TA+ Sbjct: 125 GLVPVFCCGEPLEVREAGTYVEHVVAQVKAGLEGLEIADPAQLVVAYEPIWAIGTGMTAT 184 Query: 181 SDQAEEMCKTIRETVKDLYNEETAENVRIQYGGSVKPANVKELMAKPNIDGGLVGGASLV 240 +D A+E+C +RE + DL+ E A +R+ YGGS KP N+ EL AKP++DG LVGGASL Sbjct: 185 ADDAQEVCAAVREALADLFGAELASGIRVLYGGSAKPGNIAELTAKPDVDGALVGGASLK 244 Query: 241 PDSYLALV 248 + +V Sbjct: 245 AADFSQMV 252 Lambda K H 0.312 0.130 0.377 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: 174 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: 252 Length of database: 257 Length adjustment: 24 Effective length of query: 228 Effective length of database: 233 Effective search space: 53124 Effective search space used: 53124 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 47 (22.7 bits)
Align candidate WP_009140074.1 HMPREF9452_RS00185 (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.2990586.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-60 191.1 1.6 1.5e-60 190.8 1.6 1.0 1 NCBI__GCF_000225705.1:WP_009140074.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000225705.1:WP_009140074.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 190.8 1.6 1.5e-60 1.5e-60 1 227 [. 9 245 .. 9 246 .. 0.95 Alignments for each domain: == domain 1 score: 190.8 bits; conditional E-value: 1.5e-60 TIGR00419 1 lviinfKlnesvgkvelevaklaeevasea.gvevavappfvdldvvkdeve.seiqvaAqnvdavksGaftG 71 l+ +n+K+n+ v+ +++ +l + + +++ gvev v pp +dl +v+ +++ s i+++Aqnv +Ga+tG NCBI__GCF_000225705.1:WP_009140074.1 9 LIAGNWKMNNDVQAAATLADELVAALDGVDnGVEVLVCPPTIDLTTVAAKLDgSAIKLGAQNVYWEAAGAYTG 81 689*********************99987538********************9******************** PP TIGR00419 72 eisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaa 144 e s +mlk +G+ + +igHsErR +++e+de +kk l + gl +v C ge le rea++ ++ v + +a NCBI__GCF_000225705.1:WP_009140074.1 82 ESSCDMLKSAGCTYCIIGHSERRDYFHETDEDQNKKAKALVAAGLVPVFCCGEPLEVREAGTYVEHVVAQVKA 154 *******************************************************************999998 PP TIGR00419 145 aA.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvlyGasvtaaedael 209 + vvA+EP+++iGtG++++ +a++v + vr+ l+ +e+a +rvlyG+s + ++ ael NCBI__GCF_000225705.1:WP_009140074.1 155 GLegleiadPAQLVVAYEPIWAIGTGMTATADDAQEVCAAVREALADlFGAELASGIRVLYGGSAKPGNIAEL 227 66676664556779********************************9899*********************** PP TIGR00419 210 aaqldvdGvLlasavlka 227 a++dvdG+L+++a+lka NCBI__GCF_000225705.1:WP_009140074.1 228 TAKPDVDGALVGGASLKA 245 *****************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (257 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: 13.19 // [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