Align L-rhamnose isomerase (EC 5.3.1.14) (characterized)
to candidate WP_064574663.1 M988_RS14420 L-rhamnose isomerase
Query= BRENDA::P32170 (419 letters) >NCBI__GCF_001655005.1:WP_064574663.1 Length = 418 Score = 752 bits (1941), Expect = 0.0 Identities = 357/418 (85%), Positives = 394/418 (94%) Query: 1 MTTQLEQAWELAKQRFAAVGIDVEEALRQLDRLPVSMHCWQGDDVSGFENPEGSLTGGIQ 60 MTT ++QAWELAKQRF+AVG+DVE AL+ +++LPVSMHCWQGDDV+GFENPEGSLTGGIQ Sbjct: 1 MTTLIDQAWELAKQRFSAVGVDVENALKTMEQLPVSMHCWQGDDVAGFENPEGSLTGGIQ 60 Query: 61 ATGNYPGKARNASELRADLEQAMRLIPGPKRLNLHAIYLESDTPVSRDQIKPEHFKNWVE 120 ATGNYPGKARNA+ELR+DLE A+ LIPGPKRLNLHAIYLESDTPV+R++I+P HF +WVE Sbjct: 61 ATGNYPGKARNAAELRSDLEMALSLIPGPKRLNLHAIYLESDTPVARNKIEPRHFAHWVE 120 Query: 121 WAKANQLGLDFNPSCFSHPLSADGFTLSHADDSIRQFWIDHCKASRRVSAYFGEQLGTPS 180 WAK + LGLDFNPSCFSHPLSADGFTLS +D IRQFWI+HC+ASRR+SAYFGEQLGTPS Sbjct: 121 WAKKHHLGLDFNPSCFSHPLSADGFTLSSSDPEIRQFWIEHCQASRRISAYFGEQLGTPS 180 Query: 181 VMNIWIPDGMKDITVDRLAPRQRLLAALDEVISEKLNPAHHIDAVESKLFGIGAESYTVG 240 VMNIWIPDGMKD +DRLAPRQRL +ALDEVISEKLNPAHHIDAVESKLFGIGAESYTVG Sbjct: 181 VMNIWIPDGMKDTPIDRLAPRQRLASALDEVISEKLNPAHHIDAVESKLFGIGAESYTVG 240 Query: 241 SNEFYMGYATSRQTALCLDAGHFHPTEVISDKISAAMLYVPQLLLHVSRPVRWDSDHVVL 300 SNEFY+GYA SRQTALCLDAGHFHPTEVISDKIS+AMLYVP+LLLHVSRPVRWDSDHVVL Sbjct: 241 SNEFYLGYAASRQTALCLDAGHFHPTEVISDKISSAMLYVPRLLLHVSRPVRWDSDHVVL 300 Query: 301 LDDETQAIASEIVRHDLFDRVHIGLDFFDASINRIAAWVIGTRNMKKALLRALLEPTAEL 360 LDDETQAIA+EIVRHDLFDRVHIGLDFFDASINRIAAWVIGTRNMKKALLRALLEPT L Sbjct: 301 LDDETQAIANEIVRHDLFDRVHIGLDFFDASINRIAAWVIGTRNMKKALLRALLEPTEHL 360 Query: 361 RKLEAAGDYTARLALLEEQKSLPWQAVWEMYCQRHDTPAGSEWLESVRAYEKEILSRR 418 R+LE +GDYTARLALLEEQKSLPWQAVWEMYCQR+D PA + WL +VR YE+++LS+R Sbjct: 361 RELEESGDYTARLALLEEQKSLPWQAVWEMYCQRNDVPADARWLNAVREYEEQVLSQR 418 Lambda K H 0.319 0.134 0.410 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: 701 Number of extensions: 18 Number of successful extensions: 1 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: 419 Length of database: 418 Length adjustment: 32 Effective length of query: 387 Effective length of database: 386 Effective search space: 149382 Effective search space used: 149382 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: 50 (23.9 bits)
Align candidate WP_064574663.1 M988_RS14420 (L-rhamnose isomerase)
to HMM TIGR01748 (rhaA: L-rhamnose isomerase (EC 5.3.1.14))
# 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/TIGR01748.hmm # target sequence database: /tmp/gapView.2756172.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01748 [M=414] Accession: TIGR01748 Description: rhaA: L-rhamnose 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-242 790.8 0.0 1.9e-242 790.6 0.0 1.0 1 NCBI__GCF_001655005.1:WP_064574663.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001655005.1:WP_064574663.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 790.6 0.0 1.9e-242 1.9e-242 1 414 [] 5 418 .] 5 418 .] 1.00 Alignments for each domain: == domain 1 score: 790.6 bits; conditional E-value: 1.9e-242 TIGR01748 1 iekayevakqryeavgidveealrqledvkislhcwqgddvegfenpegeltggiqatgnypgkartaeelrr 73 i++a+e+akqr++avg+dve+al+++e++++s+hcwqgddv gfenpeg+ltggiqatgnypgkar+a elr NCBI__GCF_001655005.1:WP_064574663.1 5 IDQAWELAKQRFSAVGVDVENALKTMEQLPVSMHCWQGDDVAGFENPEGSLTGGIQATGNYPGKARNAAELRS 77 789********************************************************************** PP TIGR01748 74 dlekalslipgkkrlnlhaiyvetdekverdeikpkhfknwvewakeqglgldfnptlfshelaadgltlsha 146 dle alslipg+krlnlhaiy+e+d++v r++i+p+hf wvewak++ lgldfnp++fsh+l+adg+tls++ NCBI__GCF_001655005.1:WP_064574663.1 78 DLEMALSLIPGPKRLNLHAIYLESDTPVARNKIEPRHFAHWVEWAKKHHLGLDFNPSCFSHPLSADGFTLSSS 150 ************************************************************************* PP TIGR01748 147 dkeirefwiehckasrriseyfgkelgtpsvtniwipdglkdipvdrltprkrllealdevlsekldekytld 219 d+eir+fwiehc+asrris+yfg++lgtpsv+niwipdg+kd p+drl+pr+rl aldev+sekl++++++d NCBI__GCF_001655005.1:WP_064574663.1 151 DPEIRQFWIEHCQASRRISAYFGEQLGTPSVMNIWIPDGMKDTPIDRLAPRQRLASALDEVISEKLNPAHHID 223 ************************************************************************* PP TIGR01748 220 avesklfglgaesytvgshefylgyaltrdklllldaghfhptevisnkisslllyskklllhvsrpvrwdsd 292 avesklfg+gaesytvgs+efylgya +r+++l+ldaghfhptevis+kiss++ly+++lllhvsrpvrwdsd NCBI__GCF_001655005.1:WP_064574663.1 224 AVESKLFGIGAESYTVGSNEFYLGYAASRQTALCLDAGHFHPTEVISDKISSAMLYVPRLLLHVSRPVRWDSD 296 ************************************************************************* PP TIGR01748 293 hvvvlddelreiaseivrndllekvaigldffdasinriaawvigtrnmkkallkalleptadlkkleeegdy 365 hvv+ldde+++ia+eivr+dl+++v+igldffdasinriaawvigtrnmkkall+allept +l++lee gdy NCBI__GCF_001655005.1:WP_064574663.1 297 HVVLLDDETQAIANEIVRHDLFDRVHIGLDFFDASINRIAAWVIGTRNMKKALLRALLEPTEHLRELEESGDY 369 ************************************************************************* PP TIGR01748 366 terlalleelkslpfgavwesycerkgvpvgeewlkevkayekevllkr 414 t+rlallee+kslp++avwe+yc+r++vp++ wl+ v++ye++vl++r NCBI__GCF_001655005.1:WP_064574663.1 370 TARLALLEEQKSLPWQAVWEMYCQRNDVPADARWLNAVREYEEQVLSQR 418 **********************************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (414 nodes) Target sequences: 1 (418 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 15.55 // [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