Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_018125209.1 B149_RS0110990 triose-phosphate isomerase
Query= SwissProt::Q5SJR1 (250 letters) >NCBI__GCF_000375485.1:WP_018125209.1 Length = 251 Score = 184 bits (468), Expect = 1e-51 Identities = 105/247 (42%), Positives = 144/247 (58%), Gaps = 6/247 (2%) Query: 5 LVAGNWKMHKTPSEARVWFAELKRLLP---PLQSEAAVLPAFPILPVAKEVLAETQVGY- 60 L+A NWKM+K ++A EL++L+ P E + P F + E + Q + Sbjct: 4 LMAANWKMYKNRADALSTAQELRKLVSDKLPEDREVLIFPPFTSIDRVAEAFSGAQGFHV 63 Query: 61 GAQDVSAHKEGAYTGEVSARMLSDLGCRYAIVGHSERRRYHGETDALVAEKAKRLLEEGI 120 G QD H+EGAYTGE+S ML D G + + GHSERR GE D LV +K L++G+ Sbjct: 64 GGQDYYLHEEGAYTGEISPSMLKDAGAGWGLTGHSERRHVLGEDDELVGQKTAYGLQQGL 123 Query: 121 TPILCVGEPLEVREKGEAVPYTLRQLRGSLEGVEPP-GPEALVIAYEPVWAIGTGKNATP 179 LC+GE +E R+ G+ RQL + V+ P L +AYEPVWAIGTG+ A Sbjct: 124 NVCLCIGETIEQRKGGKVQEVIDRQLAAGVRNVDRDLDPARLAVAYEPVWAIGTGEVAGS 183 Query: 180 EDAEAMHQAIRKALSERYGEAFASRVRILYGGSVNPKNFADLLSMPNVDGGLVGGASLEL 239 E+ E H RK L E +G+ A+ +RILYGGSV P N + ++S+ NVDG LVGGASL Sbjct: 184 EEIEEAHGLTRKKLLELFGDK-ANEIRILYGGSVKPANVSGIISLDNVDGVLVGGASLAS 242 Query: 240 ESFLALL 246 +SF ++ Sbjct: 243 DSFAEIV 249 Lambda K H 0.317 0.135 0.393 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: 192 Number of extensions: 14 Number of successful extensions: 4 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: 250 Length of database: 251 Length adjustment: 24 Effective length of query: 226 Effective length of database: 227 Effective search space: 51302 Effective search space used: 51302 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_018125209.1 B149_RS0110990 (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.15460.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-49 153.7 0.0 4e-49 153.5 0.0 1.0 1 lcl|NCBI__GCF_000375485.1:WP_018125209.1 B149_RS0110990 triose-phosphate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000375485.1:WP_018125209.1 B149_RS0110990 triose-phosphate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 153.5 0.0 4e-49 4e-49 2 227 .. 5 242 .. 4 243 .. 0.92 Alignments for each domain: == domain 1 score: 153.5 bits; conditional E-value: 4e-49 TIGR00419 2 viinfKlnesvgkvelevaklaeevase..agvevavappfvdldvvkdeve..seiqvaAqnvdavks 66 + n+K+ + + ++l++ v+++ ++ ev + ppf +d+v+++ + +v+ q+ +++ lcl|NCBI__GCF_000375485.1:WP_018125209.1 5 MAANWKMYKNRADALSTAQELRKLVSDKlpEDREVLIFPPFTSIDRVAEAFSgaQGFHVGGQDYYLHEE 73 578***7777777777788899999986336889****************9976679************ PP TIGR00419 67 GaftGeisAemlkdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaarti 135 Ga+tGeis mlkd+Ga + l gHsErR +l e del+++k a+ ++gl++ +C+get e+r+ ++ lcl|NCBI__GCF_000375485.1:WP_018125209.1 74 GAYTGEISPSMLKDAGAGWGLTGHSERRHVLGEDDELVGQKTAYGLQQGLNVCLCIGETIEQRKGGKVQ 142 *****************************************************************9999 PP TIGR00419 136 nnvattaaaaA......lepd..vvAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvl 196 +++ ++ aa l+p+ vA+EPv++iGtG ++ e e+ ++ r l + + a+++r+l lcl|NCBI__GCF_000375485.1:WP_018125209.1 143 EVIDRQLAAGVrnvdrdLDPArlAVAYEPVWAIGTGEVAGSEEIEEAHGLTRKKLLELFGDKANEIRIL 211 99988888777899999777633799*******************************99999******* PP TIGR00419 197 yGasvtaaedaelaaqldvdGvLlasavlka 227 yG+sv+ a+ + +vdGvL+++a+l + lcl|NCBI__GCF_000375485.1:WP_018125209.1 212 YGGSVKPANVSGIISLDNVDGVLVGGASLAS 242 *********999999999**********976 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 7.61 // [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