Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate 349657 BT0129 mannonate dehydratase (NCBI ptt file)
Query= BRENDA::P24215 (394 letters) >FitnessBrowser__Btheta:349657 Length = 395 Score = 345 bits (884), Expect = 2e-99 Identities = 183/390 (46%), Positives = 246/390 (63%), Gaps = 17/390 (4%) Query: 1 MEQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWS 60 ME+TWRW+G D ++L +RQ G G+VTALH IPNGE+W++E I K+ IE GL WS Sbjct: 2 MEKTWRWFGKKDKITLPMLRQIGVEGIVTALHDIPNGEIWTIEAINALKSYIESYGLRWS 61 Query: 61 VVESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLP 120 VVES+P+ E IK EQ I NY+ +L NL +CGI+TVCYNFMPV+DW RTDL+Y+ P Sbjct: 62 VVESLPVCEAIKYGGTEREQLIENYKVSLTNLGKCGIKTVCYNFMPVIDWIRTDLQYLCP 121 Query: 121 DGSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAG 180 DG+ +L +D+I FA F+M IL+R GAE DYTEEE+ + +E +++++K L II Sbjct: 122 DGTSSLYYDRIRFAYFDMKILEREGAEKDYTEEELHKVSELDQVITEKEKDDLIDTIIVK 181 Query: 181 LPGAEEGYTLD-------QFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVH 233 G G + F++ L LYKDI++ LREN FL AI+PV EE GV M VH Sbjct: 182 TQGFVNGNIKEGDKEPVVLFKRLLTLYKDINRDILRENMCHFLSAIMPVCEEYGVNMCVH 241 Query: 234 PDDPPRPILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPR 293 PDDPP +LGLPRIV+ ED+ W ++ V++ NG T C GS ND ++ K+F R Sbjct: 242 PDDPPFQVLGLPRIVTNEEDIAWFLNAVDNPHNGLTFCAGSLSAGEHNDTRELAKKFAKR 301 Query: 294 IYFTHLRSTMREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHG 353 +F HLRST F E++HL G + ++++ I E+E+ +PMR DHG Sbjct: 302 THFIHLRSTAAMPG-GNFIESSHLAGRGHIIDLIR-IFEKENPG--------LPMRIDHG 351 Query: 354 HQMLDDLKKKTNPGYSAIGRLKGLAEVRGV 383 ML D K NPGYS GR+ LA+V G+ Sbjct: 352 RMMLGDEDKGYNPGYSFYGRMLALAQVEGM 381 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: 462 Number of extensions: 17 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: 394 Length of database: 395 Length adjustment: 31 Effective length of query: 363 Effective length of database: 364 Effective search space: 132132 Effective search space used: 132132 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 349657 BT0129 (mannonate dehydratase (NCBI ptt file))
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.13187.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-134 433.0 0.0 7.1e-134 432.7 0.0 1.0 1 lcl|FitnessBrowser__Btheta:349657 BT0129 mannonate dehydratase (NC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:349657 BT0129 mannonate dehydratase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 432.7 0.0 7.1e-134 7.1e-134 1 389 [. 2 387 .. 2 392 .. 0.95 Alignments for each domain: == domain 1 score: 432.7 bits; conditional E-value: 7.1e-134 TIGR00695 1 meqtfrwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheeiklqte 76 me+t+rw+G++d ++l +rq+G++Givtalh+ipnGe+w +e i++ k++ie++Gl +svves+pv e+ik + lcl|FitnessBrowser__Btheta:349657 2 MEKTWRWFGKKDKITLPMLRQIGVEGIVTALHDIPNGEIWTIEAINALKSYIESYGLRWSVVESLPVCEAIKYGGT 77 9*************************************************************************** PP TIGR00695 77 eyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalelhilkrpdaekdyte 152 e+e+ ienyk +l nl +cGik+vcynfmpv+dw rtdl+y +dG+ +l++d+i++a ++++il+r +aekdyte lcl|FitnessBrowser__Btheta:349657 78 EREQLIENYKVSLTNLGKCGIKTVCYNFMPVIDWIRTDLQYLCPDGTSSLYYDRIRFAYFDMKILEREGAEKDYTE 153 **************************************************************************** PP TIGR00695 153 eelvraveeasdmseedkarltrniiaglpGaeeg.....ek..ldrikelleaykdideeklrenlafflkeilp 221 eel + e + ++e++k l ii G+ +g +k + +k+ll +ykdi+++ lren++ fl +i+p lcl|FitnessBrowser__Btheta:349657 154 EELHKVSELDQVITEKEKDDLIDTIIVKTQGFVNGnikegDKepVVLFKRLLTLYKDINRDILRENMCHFLSAIMP 229 **************************9998876652111132225679**************************** PP TIGR00695 222 vaeevGvkmaihpddpprpilGlprivstiedmkklveisdspangitlctGsyGvradndlvelakqfadriyfa 297 v ee+Gv+m +hpddpp +lGlpriv+ +ed+ ++ + +d p ng+t+c+Gs+ + nd elak+fa+r +f lcl|FitnessBrowser__Btheta:349657 230 VCEEYGVNMCVHPDDPPFQVLGLPRIVTNEEDIAWFLNAVDNPHNGLTFCAGSLSAGEHNDTRELAKKFAKRTHFI 305 **************************************************************************** PP TIGR00695 298 hlrsvkreenpktfheaahlekdvdlyevvkavleeehrrkaeGkedlipvrpdhGrqllddlkkktnpGysaigr 373 hlrs+ + +f+e++hl + + + ++++ + +++ G +p+r dhGr +l+d k npGys +gr lcl|FitnessBrowser__Btheta:349657 306 HLRSTAAMPGG-NFIESSHLAGRGHIIDLIR-----IFEKENPG----LPMRIDHGRMMLGDEDKGYNPGYSFYGR 371 *******9999.***************9987.....46678899....9*************************** PP TIGR00695 374 lkGlaelrGlelalkk 389 ++ la+++G+ + ++ lcl|FitnessBrowser__Btheta:349657 372 MLALAQVEGMMTVVDD 387 *********9987765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (395 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: 8.76 // [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