Align Myo-inosose-2 dehydratase (EC 4.2.1.44) (characterized)
to candidate WP_004124227.1 RHSP_RS23485 myo-inosose-2 dehydratase
Query= reanno::HerbieS:HSERO_RS12135 (306 letters) >NCBI__GCF_000359745.1:WP_004124227.1 Length = 301 Score = 267 bits (682), Expect = 3e-76 Identities = 143/296 (48%), Positives = 184/296 (62%), Gaps = 4/296 (1%) Query: 4 PFNVKIGINPISWMNDDLPSLGGETPLEQALSEGAEIGYRGFELGNKFPRQPEALRAVLG 63 P V++ ++P+SW ND L LG + +E L++ + GY+G ELG KFPR E LR +LG Sbjct: 6 PMGVRLAVSPLSWANDVLEDLGADITVETCLADASGTGYQGIELGRKFPRDAEVLRPLLG 65 Query: 64 KYQLECVSGWYSGQLATRSVEEEIVAVEAHLNLLAANGAQVMVYGEVADSIQGAPT--PL 121 Y L SGW+SG+LA RSV+EE+ AV +H LL A G QVMVYGEVA G+P P+ Sbjct: 66 NYGLSLASGWHSGELAERSVDEEMAAVASHARLLRAMGCQVMVYGEVAMMSPGSPLDQPM 125 Query: 122 YQRPRFGSEAAWQGYAQRLDQFARHLL-QRGVRLAYHHHMGAYVETPEDLDKLMALTGEE 180 QR E GYA RL +F+ LL + G++LAYHHH+ ET ++ +L L G E Sbjct: 126 SQRMIMPKEDV-PGYAARLTEFSIRLLGEYGLKLAYHHHLMMVAETYGEISRLFDLAGNE 184 Query: 181 VGLLFDSGHIAFAGGDPLAVLQRHLDRVCHVHCKDVRPAVVKLARNRDWSFLQAVINGAF 240 GLL D+GH A G D ++ R DR+ H+H KDVR AV+ R RD SF V G F Sbjct: 185 TGLLLDTGHCAGGGFDYRRLIDRFGDRIVHIHLKDVRGAVMDEVRQRDLSFNTGVRRGMF 244 Query: 241 TVPGDGAIDFAPLLQLLYRRGYSGWLVVEAEQDPAVAPSYRYAQMGYRHLSTLVAA 296 TVPGDG IDF+PL + + GY GWLVVEAEQDPAVAP+ +H+S + A Sbjct: 245 TVPGDGNIDFSPLARFVRDSGYQGWLVVEAEQDPAVAPARAAVTRAVQHVSKVFEA 300 Lambda K H 0.320 0.137 0.417 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: 291 Number of extensions: 11 Number of successful extensions: 3 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: 306 Length of database: 301 Length adjustment: 27 Effective length of query: 279 Effective length of database: 274 Effective search space: 76446 Effective search space used: 76446 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
Align candidate WP_004124227.1 RHSP_RS23485 (myo-inosose-2 dehydratase)
to HMM TIGR04379 (iolE: myo-inosose-2 dehydratase (EC 4.2.1.44))
# 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/TIGR04379.hmm # target sequence database: /tmp/gapView.1955908.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR04379 [M=290] Accession: TIGR04379 Description: myo_inos_iolE: myo-inosose-2 dehydratase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-99 318.2 0.0 3.4e-99 318.0 0.0 1.0 1 NCBI__GCF_000359745.1:WP_004124227.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000359745.1:WP_004124227.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 318.0 0.0 3.4e-99 3.4e-99 2 288 .. 9 296 .. 8 298 .. 0.97 Alignments for each domain: == domain 1 score: 318.0 bits; conditional E-value: 3.4e-99 TIGR04379 2 vklgiaPiaWvndDlpelggdttleqvlseaaeagfsgtElgnkfpkdpavLkaaleerglelvsgwfsalll 74 v+l+++P++W nd l++lg+d+t+e++l++a+ g++g+Elg+kfp+d++vL+++l ++gl+l+sgw s++l+ NCBI__GCF_000359745.1:WP_004124227.1 9 VRLAVSPLSWANDVLEDLGADITVETCLADASGTGYQGIELGRKFPRDAEVLRPLLGNYGLSLASGWHSGELA 81 89*********************************************************************** PP TIGR04379 75 eksveeeieavrehlellkalgakvivvaEvgksiqgdk.dtplaerpklteeeweelaeklnklg.eilkek 145 e+sv+ee++av++h++ll+a+g++v+v++Ev+ g++ d+p+++r+ + +e++ +a++l++++ ++l e+ NCBI__GCF_000359745.1:WP_004124227.1 82 ERSVDEEMAAVASHARLLRAMGCQVMVYGEVAMMSPGSPlDQPMSQRMIMPKEDVPGYAARLTEFSiRLLGEY 154 ********************************98777653899**********************845677** PP TIGR04379 146 glklayHhHlgtvveteeeidrlmeltdpelvgllyDtGHlvfagedplavlekyadRiahvHlKDvRkevle 218 glklayHhHl v et ei rl +l+++e gll+DtGH + +g d+ +++++++dRi+h+HlKDvR +v++ NCBI__GCF_000359745.1:WP_004124227.1 155 GLKLAYHHHLMMVAETYGEISRLFDLAGNE-TGLLLDTGHCAGGGFDYRRLIDRFGDRIVHIHLKDVRGAVMD 226 ****************************99.9***************************************** PP TIGR04379 219 evrkekksFldavlkGvftvPGdGcidfeeilealkakdYeGWlvvEaEqDPakaepleyakkakkylee 288 evr+++ sF ++v++G+ftvPGdG idf+++++ ++ ++Y+GWlvvEaEqDPa+a++ + + a +++++ NCBI__GCF_000359745.1:WP_004124227.1 227 EVRQRDLSFNTGVRRGMFTVPGDGNIDFSPLARFVRDSGYQGWLVVEAEQDPAVAPARAAVTRAVQHVSK 296 *********************************************************9999999999887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (290 nodes) Target sequences: 1 (301 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: 13.23 // [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