Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate 350960 BT1432 mannonate dehydratase (NCBI ptt file)
Query= BRENDA::P24215 (394 letters) >FitnessBrowser__Btheta:350960 Length = 389 Score = 520 bits (1340), Expect = e-152 Identities = 245/389 (62%), Positives = 309/389 (79%), Gaps = 6/389 (1%) Query: 2 EQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWSV 61 EQTWRWYGPNDPVSL D++QAGATG+V ALHHIPNGEVW+VEEI+KRK +IE+ GL WSV Sbjct: 5 EQTWRWYGPNDPVSLWDIKQAGATGIVNALHHIPNGEVWTVEEIMKRKQMIEEVGLTWSV 64 Query: 62 VESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLPD 121 VESVP+HE IKT TG Y ++I NY++++RNLA+CG+ V YNFMPVLDWTRTDL Y +PD Sbjct: 65 VESVPVHEHIKTQTGEYLKYIENYKESIRNLAKCGVMVVTYNFMPVLDWTRTDLAYTMPD 124 Query: 122 GSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAGL 181 GSKALRF++ F AF++ ILKRP AE DYT EEIA+A RF MS++DK L RN+IAGL Sbjct: 125 GSKALRFEKAAFLAFDLFILKRPNAEKDYTPEEIAKAKARFEQMSEDDKKLLVRNMIAGL 184 Query: 182 PGAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRPI 241 PG+EE +T++QF++ L+ Y DID KLR N FLK I PVA+EVGV++ +HPDDPP I Sbjct: 185 PGSEESFTVEQFQEALDRYNDIDAEKLRSNLIFFLKEIAPVADEVGVKLVIHPDDPPYTI 244 Query: 242 LGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLRS 301 LGLPRI+ST ED + +++ V + +NG +CTGS+GVRADNDL M+++FG R+ F HLRS Sbjct: 245 LGLPRILSTEEDFKKLIEAVPNESNGLCLCTGSFGVRADNDLAGMMERFGDRVNFVHLRS 304 Query: 302 TMREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDLK 361 T R D F+EA HL G+VDMY V+K+++ + RRK I MRPDHGHQM+DDLK Sbjct: 305 TQR-DEEGNFYEANHLEGNVDMYNVMKSLILLQQRRKCS-----IAMRPDHGHQMIDDLK 358 Query: 362 KKTNPGYSAIGRLKGLAEVRGVELAIQRA 390 KKTNPGYS +GRL+GLAE+RG+E+ I ++ Sbjct: 359 KKTNPGYSCLGRLRGLAELRGLEMGIAKS 387 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: 539 Number of extensions: 22 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: 389 Length adjustment: 31 Effective length of query: 363 Effective length of database: 358 Effective search space: 129954 Effective search space used: 129954 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 350960 BT1432 (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.28779.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-187 607.4 0.0 7.1e-187 607.2 0.0 1.0 1 lcl|FitnessBrowser__Btheta:350960 BT1432 mannonate dehydratase (NC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:350960 BT1432 mannonate dehydratase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 607.2 0.0 7.1e-187 7.1e-187 2 389 .. 5 386 .. 4 389 .] 0.99 Alignments for each domain: == domain 1 score: 607.2 bits; conditional E-value: 7.1e-187 TIGR00695 2 eqtfrwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheeiklqtee 77 eqt+rwyG+ndpvsl d++qaGa+Giv alhhipnGevw veei krk++ie++Gl++svvesvpvhe+ik+qt+e lcl|FitnessBrowser__Btheta:350960 5 EQTWRWYGPNDPVSLWDIKQAGATGIVNALHHIPNGEVWTVEEIMKRKQMIEEVGLTWSVVESVPVHEHIKTQTGE 80 89************************************************************************** PP TIGR00695 78 yekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalelhilkrpdaekdytee 153 y kyienyk+++rnla+cG+ vv ynfmpvldwtrtdlay+++dGskalrf+k+++ a++l+ilkrp+aekdyt e lcl|FitnessBrowser__Btheta:350960 81 YLKYIENYKESIRNLAKCGVMVVTYNFMPVLDWTRTDLAYTMPDGSKALRFEKAAFLAFDLFILKRPNAEKDYTPE 156 **************************************************************************** PP TIGR00695 154 elvraveeasdmseedkarltrniiaglpGaeegekldrikelleaykdideeklrenlafflkeilpvaeevGvk 229 e+++a+ ++++mse+dk l+rn+iaglpG ee ++++++e l++y+did eklr nl fflkei pva+evGvk lcl|FitnessBrowser__Btheta:350960 157 EIAKAKARFEQMSEDDKKLLVRNMIAGLPGSEESFTVEQFQEALDRYNDIDAEKLRSNLIFFLKEIAPVADEVGVK 232 **************************************************************************** PP TIGR00695 230 maihpddpprpilGlprivstiedmkklveisdspangitlctGsyGvradndlvelakqfadriyfahlrsvkre 305 + ihpddpp+ ilGlpri+st+ed+kkl+e ++ +ng+ lctGs+Gvradndl ++++f+dr+ f hlrs++r+ lcl|FitnessBrowser__Btheta:350960 233 LVIHPDDPPYTILGLPRILSTEEDFKKLIEAVPNESNGLCLCTGSFGVRADNDLAGMMERFGDRVNFVHLRSTQRD 308 **************************************************************************** PP TIGR00695 306 enpktfheaahlekdvdlyevvkavleeehrrkaeGkedlipvrpdhGrqllddlkkktnpGysaigrlkGlaelr 381 e++ +f+ea hle++vd+y+v+k+++ + rrk i +rpdhG+q++ddlkkktnpGys +grl+Glaelr lcl|FitnessBrowser__Btheta:350960 309 EEG-NFYEANHLEGNVDMYNVMKSLILLQQRRKCS-----IAMRPDHGHQMIDDLKKKTNPGYSCLGRLRGLAELR 378 ***.**********************988888765.....68********************************** PP TIGR00695 382 Glelalkk 389 Gle+ + k lcl|FitnessBrowser__Btheta:350960 379 GLEMGIAK 386 ****9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (389 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 7.95 // [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