Align triosephosphate isomerase subunit (EC 5.3.1.1) (characterized)
to candidate WP_013451423.1 CALNI_RS06530 triose-phosphate isomerase
Query= metacyc::MONOMER-13051 (252 letters) >NCBI__GCF_000183405.1:WP_013451423.1 Length = 251 Score = 241 bits (614), Expect = 1e-68 Identities = 123/250 (49%), Positives = 168/250 (67%), Gaps = 2/250 (0%) Query: 3 RTPIIAGNWKLNMNPKETVEFVNAVKDQLPDPSKVESVICAPAVDLDALLKAAEGSNLHV 62 R +IA NWK+N+ + + FV++ K+ D K++ +I P L L KA + N + Sbjct: 2 RRSLIAANWKMNLTFDDALSFVSSFKEFKFDTKKIDVLIAPPFPYLSDLGKALKKINKKI 61 Query: 63 --GAENCYWENSGAFTGETSPAVLKEMGVQYVIIGHSERRDYFHETDEDINKKAKAIFAN 120 A+N ++E+SGA+TGE S +LK +G+ + IIGHSERR YF +TD +NKK K N Sbjct: 62 ILSAQNIHFESSGAYTGEVSAEMLKSIGINWTIIGHSERRQYFGDTDIIVNKKVKKALEN 121 Query: 121 GLTPILCCGESLETREAGKENEWVVSQIKAGLEGLTSEQVSKLVIAYEPIWAIGTGKTAS 180 GL ILC GE L REAG E E V+SQ+ L G+ S+ +S++VIAYEP+WAIGTGKTA Sbjct: 122 GLNVILCVGEQLPEREAGIEKELVISQLGMALYGVESDNISRIVIAYEPVWAIGTGKTAR 181 Query: 181 SDQAEEMCKTIRETVKDLYNEETAENVRIQYGGSVKPANVKELMAKPNIDGGLVGGASLV 240 S AEEM ++IRE ++ Y + A NVRI YGGSVKP N+ +LM+ PNIDG LVGGASL Sbjct: 182 SSDAEEMHRSIREYIRSKYGRKIANNVRIIYGGSVKPDNISDLMSMPNIDGALVGGASLK 241 Query: 241 PDSYLALVNY 250 +S+ +++Y Sbjct: 242 FESFAKIISY 251 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: 162 Number of extensions: 4 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: 251 Length adjustment: 24 Effective length of query: 228 Effective length of database: 227 Effective search space: 51756 Effective search space used: 51756 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: 46 (22.3 bits)
Align candidate WP_013451423.1 CALNI_RS06530 (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.14067.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-65 204.7 0.0 1e-64 204.5 0.0 1.0 1 lcl|NCBI__GCF_000183405.1:WP_013451423.1 CALNI_RS06530 triose-phosphate i Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000183405.1:WP_013451423.1 CALNI_RS06530 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 204.5 0.0 1e-64 1e-64 1 227 [. 5 242 .. 5 243 .. 0.95 Alignments for each domain: == domain 1 score: 204.5 bits; conditional E-value: 1e-64 TIGR00419 1 lviinfKlnesvgkvelevaklaeevaseagvevavappfvdld...vvkdeveseiqvaAqnvdavks 66 l+ n+K+n ++ + v++ +e +++++ v +appf +l+ + ++++ +i + Aqn++ +s lcl|NCBI__GCF_000183405.1:WP_013451423.1 5 LIAANWKMNLTFDDALSFVSSFKEFKFDTKKIDVLIAPPFPYLSdlgKALKKINKKIILSAQNIHFESS 73 6889********************9999***********9887611155677889************** PP TIGR00419 67 GaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaarti 135 Ga+tGe+sAemlk +G+++++igHsErR ++ +d +++kkv ++ e gl++++Cvge l erea+ + lcl|NCBI__GCF_000183405.1:WP_013451423.1 74 GAYTGEVSAEMLKSIGINWTIIGHSERRQYFGDTDIIVNKKVKKALENGLNVILCVGEQLPEREAGIEK 142 ********************************************************************* PP TIGR00419 136 nnvattaaaaA.......lepdvvAvEPveliGtGkpvskAeaevveksvrdhlkk.vskevaesvrvl 196 + v + + a ++ v+A+EPv++iGtGk++ +ae+++ s+r++++ +++a++vr++ lcl|NCBI__GCF_000183405.1:WP_013451423.1 143 ELVISQLGMALygvesdnISRIVIAYEPVWAIGTGKTARSSDAEEMHRSIREYIRSkYGRKIANNVRII 211 ****999998888888889999********************************98799********** PP TIGR00419 197 yGasvtaaedaelaaqldvdGvLlasavlka 227 yG+sv+ + +l+ +++dG+L+++a+lk lcl|NCBI__GCF_000183405.1:WP_013451423.1 212 YGGSVKPDNISDLMSMPNIDGALVGGASLKF 242 *****************************95 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.16 // [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