Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate WP_037152525.1 RHSP_RS16605 mannonate dehydratase
Query= BRENDA::P24215 (394 letters) >NCBI__GCF_000359745.1:WP_037152525.1 Length = 396 Score = 418 bits (1075), Expect = e-121 Identities = 213/396 (53%), Positives = 274/396 (69%), Gaps = 3/396 (0%) Query: 1 MEQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWS 60 ME+ +RWYGP+DPV LA +RQAGATG+V+ALH I +G WS ++IL KA+IE AG+ WS Sbjct: 1 MEECFRWYGPDDPVPLAHIRQAGATGIVSALHQIYDGSPWSDDQILAHKALIEAAGMRWS 60 Query: 61 VVESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLP 120 VVES+P+H IK T + ++I Y+ TLR LA+ GI TVCYNFMPV+DWTRT+L L Sbjct: 61 VVESIPVHNSIKLATADSARYIGWYKDTLRALARAGIATVCYNFMPVVDWTRTELMQPLA 120 Query: 121 DGSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAG 180 +G ALRFD ++FAA+++ LKRP E Y+EE+I A ERF M R+ RN+IAG Sbjct: 121 NGGYALRFDAVDFAAYDLFALKRPHVEDSYSEEQILAARERFGRMDPAKIDRIERNLIAG 180 Query: 181 LPGAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRP 240 LP E + F L Y + L N A FLK I+PVAEEVG+R+ +HPDDP Sbjct: 181 LPATERQFNRASFLAALAEYDGMTADHLHANLARFLKEIVPVAEEVGIRLCIHPDDPAFS 240 Query: 241 ILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLR 300 + GLPRIVST D + ++ TV S ANG T CTGS+G RADNDL MI++FGPRI+F HLR Sbjct: 241 LYGLPRIVSTAADARRILATVESPANGLTFCTGSFGTRADNDLPAMIREFGPRIHFAHLR 300 Query: 301 STMREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKED-LIPMRPDHGHQMLDD 359 + RE++ +F+EA HL G D+ V+ A+++E+ RR EG+ D IP+RPDHGH + DD Sbjct: 301 NVQREED-GSFYEADHLGGSSDIPAVILALMQEQKRRLEEGRTDWQIPLRPDHGHLLADD 359 Query: 360 L-KKKTNPGYSAIGRLKGLAEVRGVELAIQRAFFSR 394 + K+K NPGYS IGRLKGLAE+RGV I A R Sbjct: 360 IGKEKINPGYSLIGRLKGLAEIRGVMQGIATAMTER 395 Lambda K H 0.320 0.136 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: 467 Number of extensions: 26 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: 394 Length of database: 396 Length adjustment: 31 Effective length of query: 363 Effective length of database: 365 Effective search space: 132495 Effective search space used: 132495 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_037152525.1 RHSP_RS16605 (mannonate dehydratase)
to HMM TIGR00695 (uxuA: mannonate dehydratase (EC 4.2.1.8))
# 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/TIGR00695.hmm # target sequence database: /tmp/gapView.2956864.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00695 [M=394] Accession: TIGR00695 Description: uxuA: mannonate 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-152 493.9 0.0 2.1e-152 493.7 0.0 1.0 1 NCBI__GCF_000359745.1:WP_037152525.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000359745.1:WP_037152525.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 493.7 0.0 2.1e-152 2.1e-152 1 391 [. 1 392 [. 1 395 [. 0.98 Alignments for each domain: == domain 1 score: 493.7 bits; conditional E-value: 2.1e-152 TIGR00695 1 meqtfrwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheeikl 73 me +frwyG++dpv l+++rqaGa+Giv alh+i G w+ ++i ++k+ ie aG+ +svves+pvh+ ikl NCBI__GCF_000359745.1:WP_037152525.1 1 MEECFRWYGPDDPVPLAHIRQAGATGIVSALHQIYDGSPWSDDQILAHKALIEAAGMRWSVVESIPVHNSIKL 73 899********************************************************************** PP TIGR00695 74 qteeyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalelhilkrpda 146 t + +yi yk tlr la+ Gi +vcynfmpv+dwtrt+l+++l +G alrfd +++aa++l+ lkrp+ NCBI__GCF_000359745.1:WP_037152525.1 74 ATADSARYIGWYKDTLRALARAGIATVCYNFMPVVDWTRTELMQPLANGGYALRFDAVDFAAYDLFALKRPHV 146 ************************************************************************* PP TIGR00695 147 ekdyteeelvraveeasdmseedkarltrniiaglpGaeegekldrikelleaykdideeklrenlafflkei 219 e +y+ee++++a+e++ m + r+ rn+iaglp +e + + + l+ y + + l+ nla flkei NCBI__GCF_000359745.1:WP_037152525.1 147 EDSYSEEQILAARERFGRMDPAKIDRIERNLIAGLPATERQFNRASFLAALAEYDGMTADHLHANLARFLKEI 219 ************************************************************************* PP TIGR00695 220 lpvaeevGvkmaihpddpprpilGlprivstiedmkklveisdspangitlctGsyGvradndlvelakqfad 292 +pvaeevG+++ ihpddp ++Glprivst +d +++ ++++spang+t+ctGs+G+radndl ++++f++ NCBI__GCF_000359745.1:WP_037152525.1 220 VPVAEEVGIRLCIHPDDPAFSLYGLPRIVSTAADARRILATVESPANGLTFCTGSFGTRADNDLPAMIREFGP 292 ************************************************************************* PP TIGR00695 293 riyfahlrsvkreenpktfheaahlekdvdlyevvkavleeehrrkaeGkedl.ipvrpdhGrqllddl.kkk 363 ri+fahlr+v+ree++ +f+ea hl + +d+ v+ a+++e+ rr +eG++d ip+rpdhG+ l dd+ k+k NCBI__GCF_000359745.1:WP_037152525.1 293 RIHFAHLRNVQREEDG-SFYEADHLGGSSDIPAVILALMQEQKRRLEEGRTDWqIPLRPDHGHLLADDIgKEK 364 ****************.*********************************99549*************96889 PP TIGR00695 364 tnpGysaigrlkGlaelrGlelalkkva 391 npGys+igrlkGlae+rG+ + + ++ NCBI__GCF_000359745.1:WP_037152525.1 365 INPGYSLIGRLKGLAEIRGVMQGIATAM 392 ********************99887765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (396 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: 25.68 // [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