Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_017541731.1 C892_RS0126430 triose-phosphate isomerase
Query= SwissProt::Q9Z520 (258 letters) >NCBI__GCF_000341205.1:WP_017541731.1 Length = 260 Score = 353 bits (907), Expect = e-102 Identities = 179/253 (70%), Positives = 202/253 (79%), Gaps = 1/253 (0%) Query: 4 RTPLMAGNWKMNLNHLEAIAHVQKLAFALADKDYDAVEVAVLAPFTDLRSVQTLVDGDKL 63 R PL+AGNWKMN NHLEAIA VQKLAFAL DYD EV VL PFTDLRSVQTLVDGDKL Sbjct: 6 RKPLIAGNWKMNNNHLEAIALVQKLAFALDAADYDRAEVVVLPPFTDLRSVQTLVDGDKL 65 Query: 64 KIKYGAQDISAHDGGAYTGEISGPMLAKLKCTYVAVGHSERRQYHAETDEIVNAKVKAAY 123 I YGAQD+S H+ GAYTGE+SGPMLAKL C+YV GHSERR+YHAE D +VNAKVKAA+ Sbjct: 66 SIAYGAQDLSRHEKGAYTGEVSGPMLAKLGCSYVLAGHSERREYHAEDDALVNAKVKAAF 125 Query: 124 KHGLTPILCVGEELDVREAGNHVEHTLAQVEGGLKDLAAEQAESVVIAYEPVWAIGTGKV 183 H +TPILCVGE L+VR+AG+ V HT AQVE +K L AEQ E +VIAYEPVWAIGTG+V Sbjct: 126 AHDITPILCVGEGLEVRKAGDQVAHTSAQVEAAVKGLTAEQVERLVIAYEPVWAIGTGEV 185 Query: 184 CGADDAQEVC-AAIRGKLAELYSQELADKVRIQYGGSVKSGNVAEIMAKPDIDGALVGGA 242 DDAQEVC AA+R LA LY + A K R+ YGGSVK N+ IMAK DIDGALVGGA Sbjct: 186 ATPDDAQEVCGAAVRATLAGLYDEATAAKTRVLYGGSVKPDNIGGIMAKADIDGALVGGA 245 Query: 243 SLDSDEFVKIVRF 255 SL +D+F K+V+F Sbjct: 246 SLKADDFAKLVKF 258 Lambda K H 0.316 0.133 0.381 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: 285 Number of extensions: 12 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: 258 Length of database: 260 Length adjustment: 24 Effective length of query: 234 Effective length of database: 236 Effective search space: 55224 Effective search space used: 55224 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_017541731.1 C892_RS0126430 (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.2762108.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-56 177.0 1.1 2.9e-56 176.8 1.1 1.0 1 NCBI__GCF_000341205.1:WP_017541731.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000341205.1:WP_017541731.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 176.8 1.1 2.9e-56 2.9e-56 1 228 [] 9 250 .. 9 250 .. 0.92 Alignments for each domain: == domain 1 score: 176.8 bits; conditional E-value: 2.9e-56 TIGR00419 1 lviinfKlnesvgkvelevaklae..evaseagvevavappfvdldvvkdeve...seiqvaAqnvdavksGa 68 l+ +n+K+n+ + +v+kla + a+ + ev+v ppf dl+ v+ v+ i +Aq++ +++Ga NCBI__GCF_000341205.1:WP_017541731.1 9 LIAGNWKMNNNHLEAIALVQKLAFalDAADYDRAEVVVLPPFTDLRSVQTLVDgdkLSIAYGAQDLSRHEKGA 81 689*******************975689********************99887532358899*********** PP TIGR00419 69 ftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvatt 141 +tGe+s ml+ lG+ +vl gHsErR +++e d l+++kv + + ++++++Cvge le r+a+ ++ + NCBI__GCF_000341205.1:WP_017541731.1 82 YTGEVSGPMLAKLGCSYVLAGHSERREYHAEDDALVNAKVKAAFAHDITPILCVGEGLEVRKAGDQVAHTSAQ 154 **************************************************************88888877777 PP TIGR00419 142 aaaaA.......lepdvvAvEPveliGtGkpvskAeaevve.ksvrdhlkk.vskevaesvrvlyGasvtaae 205 +aa e v+A+EPv++iGtG ++++ +a++v + vr l+ ++ a ++rvlyG+sv+ + NCBI__GCF_000341205.1:WP_017541731.1 155 VEAAVkgltaeqVERLVIAYEPVWAIGTGEVATPDDAQEVCgAAVRATLAGlYDEATAAKTRVLYGGSVKPDN 227 7776677777779999**********************996268*****997888899*************** PP TIGR00419 206 daelaaqldvdGvLlasavlkae 228 +a+ d+dG+L+++a+lka+ NCBI__GCF_000341205.1:WP_017541731.1 228 IGGIMAKADIDGALVGGASLKAD 250 *********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (228 nodes) Target sequences: 1 (260 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: 20.72 // [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