Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate BWI76_RS05650 BWI76_RS05650 mannonate dehydratase
Query= BRENDA::P24215 (394 letters) >FitnessBrowser__Koxy:BWI76_RS05650 Length = 394 Score = 769 bits (1985), Expect = 0.0 Identities = 371/394 (94%), Positives = 386/394 (97%) Query: 1 MEQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWS 60 MEQTWRWYGPNDPV+LADVRQAGATGVVTALHHIPNGEVW+V+EILKRKAI+E+AGLVWS Sbjct: 1 MEQTWRWYGPNDPVTLADVRQAGATGVVTALHHIPNGEVWTVDEILKRKAIVEEAGLVWS 60 Query: 61 VVESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLP 120 VVESVPIHE+IKTHTGNY QWIANYQQ+LRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLP Sbjct: 61 VVESVPIHEEIKTHTGNYAQWIANYQQSLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLP 120 Query: 121 DGSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAG 180 DGSKALRFDQIEFAAFE+HILKRPGAEADYT EE+AQA +RFA MSDEDKARLTRNIIAG Sbjct: 121 DGSKALRFDQIEFAAFELHILKRPGAEADYTAEEVAQANQRFAAMSDEDKARLTRNIIAG 180 Query: 181 LPGAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRP 240 LPGAEEGYTLDQFR+HL YKDIDKA LRENFAVF+KAIIPVAEE GVRMAVHPDDPPRP Sbjct: 181 LPGAEEGYTLDQFRQHLATYKDIDKAALRENFAVFMKAIIPVAEEAGVRMAVHPDDPPRP 240 Query: 241 ILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLR 300 ILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLR Sbjct: 241 ILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLR 300 Query: 301 STMREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDL 360 ST+RE+NPKTFHEAAHL+GDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDL Sbjct: 301 STLREENPKTFHEAAHLHGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDL 360 Query: 361 KKKTNPGYSAIGRLKGLAEVRGVELAIQRAFFSR 394 KKKTNPGYSAIGRLKGLAEVRGVELAIQRAFFSR Sbjct: 361 KKKTNPGYSAIGRLKGLAEVRGVELAIQRAFFSR 394 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: 703 Number of extensions: 23 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: 394 Length of database: 394 Length adjustment: 31 Effective length of query: 363 Effective length of database: 363 Effective search space: 131769 Effective search space used: 131769 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 BWI76_RS05650 BWI76_RS05650 (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.19076.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.5e-236 768.3 0.1 9.5e-236 768.2 0.1 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS05650 BWI76_RS05650 mannonate dehydrat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS05650 BWI76_RS05650 mannonate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 768.2 0.1 9.5e-236 9.5e-236 1 394 [] 1 394 [] 1 394 [] 1.00 Alignments for each domain: == domain 1 score: 768.2 bits; conditional E-value: 9.5e-236 TIGR00695 1 meqtfrwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheei 71 meqt+rwyG+ndpv+l+dvrqaGa+G+vtalhhipnGevw v+ei krk+++e+aGl++svvesvp+heei lcl|FitnessBrowser__Koxy:BWI76_RS05650 1 MEQTWRWYGPNDPVTLADVRQAGATGVVTALHHIPNGEVWTVDEILKRKAIVEEAGLVWSVVESVPIHEEI 71 9********************************************************************** PP TIGR00695 72 klqteeyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalelhilk 142 k++t++y ++i+ny+q+lrnlaqcGi++vcynfmpvldwtrtdl+y+l+dGskalrfd+i++aa+elhilk lcl|FitnessBrowser__Koxy:BWI76_RS05650 72 KTHTGNYAQWIANYQQSLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLPDGSKALRFDQIEFAAFELHILK 142 *********************************************************************** PP TIGR00695 143 rpdaekdyteeelvraveeasdmseedkarltrniiaglpGaeegekldrikelleaykdideeklrenla 213 rp+ae+dyt ee+++a ++++ ms+edkarltrniiaglpGaeeg++ld+++++l++ykdid++ lren+a lcl|FitnessBrowser__Koxy:BWI76_RS05650 143 RPGAEADYTAEEVAQANQRFAAMSDEDKARLTRNIIAGLPGAEEGYTLDQFRQHLATYKDIDKAALRENFA 213 *********************************************************************** PP TIGR00695 214 fflkeilpvaeevGvkmaihpddpprpilGlprivstiedmkklveisdspangitlctGsyGvradndlv 284 +f+k+i+pvaee Gv+ma+hpddpprpilGlprivstiedm+++v++++s+ang+t+ctGsyGvradndlv lcl|FitnessBrowser__Koxy:BWI76_RS05650 214 VFMKAIIPVAEEAGVRMAVHPDDPPRPILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLV 284 *********************************************************************** PP TIGR00695 285 elakqfadriyfahlrsvkreenpktfheaahlekdvdlyevvkavleeehrrkaeGkedlipvrpdhGrq 355 +++kqf++riyf+hlrs+ reenpktfheaahl++dvd+yevvka++eeehrrkaeGkedlip+rpdhG+q lcl|FitnessBrowser__Koxy:BWI76_RS05650 285 DMIKQFGPRIYFTHLRSTLREENPKTFHEAAHLHGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQ 355 *********************************************************************** PP TIGR00695 356 llddlkkktnpGysaigrlkGlaelrGlelalkkvafkk 394 +lddlkkktnpGysaigrlkGlae+rG+ela+++++f++ lcl|FitnessBrowser__Koxy:BWI76_RS05650 356 MLDDLKKKTNPGYSAIGRLKGLAEVRGVELAIQRAFFSR 394 ************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (394 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: 7.84 // [ok]
This GapMind analysis is from Sep 17 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