Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate 8499579 DvMF_0348 Triose-phosphate isomerase (RefSeq)
Query= SwissProt::Q5SJR1 (250 letters) >FitnessBrowser__Miya:8499579 Length = 251 Score = 197 bits (502), Expect = 1e-55 Identities = 113/247 (45%), Positives = 144/247 (58%), Gaps = 6/247 (2%) Query: 5 LVAGNWKMHKTPSEARVWFAELKRLLP---PLQSEAAVLPAFPIL-PVAKEVLAETQVGY 60 L+A NWKM+KT EAR A L L P E + P F L PVA + T Sbjct: 4 LMAANWKMYKTAGEARTTAASLAALTADTLPDDREVVIFPQFTALSPVADALRHATGYSV 63 Query: 61 GAQDVSAHKEGAYTGEVSARMLSDLGCRYAIVGHSERRRYHGETDALVAEKAKRLLEEGI 120 G QDV EGAYTGE+S ML D GC + + GHSERR GE+D LV K + G+ Sbjct: 64 GGQDVYPAAEGAYTGEISPGMLMDCGCAWVLTGHSERRHVIGESDELVGAKTAFSINAGL 123 Query: 121 TPILCVGEPLEVREKGEAVPYTLRQLRGSLEGVEPPG-PEALVIAYEPVWAIGTGKNATP 179 +LC+GE +E RE G RQL L GV+ P A+ +AYEPVWAIGTGK A P Sbjct: 124 KVVLCIGETIEEREAGRLGEVLERQLETGLAGVKGDAVPAAIAVAYEPVWAIGTGKVAGP 183 Query: 180 EDAEAMHQAIRKALSERYGEAFASRVRILYGGSVNPKNFADLLSMPNVDGGLVGGASLEL 239 + H +R+ L R+GE + VRILYGGSV P+N +++++ NVDG LVGGASL+ Sbjct: 184 PEIVEAHALVRQLLVARFGEGGVA-VRILYGGSVKPENAREIIALDNVDGVLVGGASLQA 242 Query: 240 ESFLALL 246 +SF ++ Sbjct: 243 DSFSRII 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: 205 Number of extensions: 11 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 8499579 DvMF_0348 (Triose-phosphate isomerase (RefSeq))
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.3684277.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-54 171.6 0.2 1.3e-54 171.4 0.2 1.0 1 FitnessBrowser__Miya:8499579 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Miya:8499579 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 171.4 0.2 1.3e-54 1.3e-54 2 228 .] 5 243 .. 4 243 .. 0.90 Alignments for each domain: == domain 1 score: 171.4 bits; conditional E-value: 1.3e-54 TIGR00419 2 viinfKlnesvgkvelevaklaeevas..eagvevavappfvdldvvkdeve..seiqvaAqnvdavksGaftGeisAeml 78 + n+K+ + g+ + a+la+ a+ +++ ev++ p+f l+ v+d+++ + +v+ q+v Ga+tGeis ml FitnessBrowser__Miya:8499579 5 MAANWKMYKTAGEARTTAASLAALTADtlPDDREVVIFPQFTALSPVADALRhaTGYSVGGQDVYPAAEGAYTGEISPGML 85 678***999**************998844589*******************9666789*********************** PP TIGR00419 79 kdlGakgvligHsErRsllkeadeliekkvarlkelglksvvCvgetleereaartinnvattaaa.aA.......lepdv 151 d+G+++vl gHsErR ++ e+del+++k a + glk+v+C+get eerea+r +++ ++ ++ A FitnessBrowser__Miya:8499579 86 MDCGCAWVLTGHSERRHVIGESDELVGAKTAFSINAGLKVVLCIGETIEEREAGRLGEVLERQLETgLAgvkgdavPAAIA 166 ****************************************************99887777665332123444454344556 PP TIGR00419 152 vAvEPveliGtGkpvskAeaevveksvrdhlkkvskevaesvrvlyGasvtaaedaelaaqldvdGvLlasavlkae 228 vA+EPv++iGtGk++ + e + ++ vr+ l e vr+lyG+sv+ +++ e +a +vdGvL+++a+l+a+ FitnessBrowser__Miya:8499579 167 VAYEPVWAIGTGKVAGPPEIVEAHALVRQLLVARFGEGGVAVRILYGGSVKPENAREIIALDNVDGVLVGGASLQAD 243 99**************************9999988999999*********************************997 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.36 // [ok]
This GapMind analysis is from Apr 09 2024. 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