Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate CA265_RS07225 CA265_RS07225 mannonate dehydratase
Query= BRENDA::P24215 (394 letters) >FitnessBrowser__Pedo557:CA265_RS07225 Length = 389 Score = 429 bits (1103), Expect = e-125 Identities = 208/387 (53%), Positives = 278/387 (71%), Gaps = 7/387 (1%) Query: 1 MEQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWS 60 +EQTWRWYGPNDPVSL DV+QAGATG+VTALHHIP+GEVW + +I +RKAIIE AGL WS Sbjct: 6 LEQTWRWYGPNDPVSLQDVKQAGATGIVTALHHIPHGEVWPLTDIQERKAIIEAAGLTWS 65 Query: 61 VVESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLP 120 VVESVP+HE IKT + ++I NY+ +LRNL+ CGI+ VCYNFMPVLDWTRT L+ + Sbjct: 66 VVESVPVHEAIKTRRADAGKYIENYKTSLRNLSACGIKIVCYNFMPVLDWTRTQLDLEMT 125 Query: 121 DGSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAG 180 DGSKAL F+ I+ A F+++ILKR GAEADY++ + +A +++T++++D A L N++ G Sbjct: 126 DGSKALYFNWIDLAIFDLYILKREGAEADYSKSILDRAEAKYSTLTEQDLADLRVNVLMG 185 Query: 181 LPGAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRP 240 +P +E L+ R + YK I L+EN FL +I V G++M +HPDDPP Sbjct: 186 IPNEKE-IELETLRNSINEYKAIGTQGLKENLKFFLSSIAEVCTTEGIKMTIHPDDPPYA 244 Query: 241 ILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLR 300 ILGLPRI ST+ED +++ V+ NG CTGS G N+ +++ R+YF HLR Sbjct: 245 ILGLPRIASTLEDFNYIIKEVDQAFNGVCFCTGSLGAGMGNNALEIFNAVKERVYFAHLR 304 Query: 301 STMREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDL 360 + +++D +F+EA HL GDV+MYE++KA+ EE R + IP RPDHGHQMLDDL Sbjct: 305 N-VKKDEDGSFYEADHLGGDVNMYEIMKALSEENALR-----DKSIPFRPDHGHQMLDDL 358 Query: 361 KKKTNPGYSAIGRLKGLAEVRGVELAI 387 K TNPGYSAIGRL+GLAE+RG+E+ + Sbjct: 359 AKVTNPGYSAIGRLRGLAELRGLEIGV 385 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: 476 Number of extensions: 14 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: 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 CA265_RS07225 CA265_RS07225 (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.378.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-155 502.9 0.0 4e-155 502.7 0.0 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS07225 CA265_RS07225 mannonate dehydrat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS07225 CA265_RS07225 mannonate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 502.7 0.0 4e-155 4e-155 1 387 [. 6 385 .. 6 389 .] 0.98 Alignments for each domain: == domain 1 score: 502.7 bits; conditional E-value: 4e-155 TIGR00695 1 meqtfrwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvh 68 +eqt+rwyG+ndpvsl+dv+qaGa+Givtalhhip Gevw +i++rk++ie aGl++svvesvpvh lcl|FitnessBrowser__Pedo557:CA265_RS07225 6 LEQTWRWYGPNDPVSLQDVKQAGATGIVTALHHIPHGEVWPLTDIQERKAIIEAAGLTWSVVESVPVH 73 59****************************************************************** PP TIGR00695 69 eeiklqteeyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaal 136 e+ik++ + +kyienyk +lrnl+ cGik+vcynfmpvldwtrt+l e+ dGskal+f+ i++a + lcl|FitnessBrowser__Pedo557:CA265_RS07225 74 EAIKTRRADAGKYIENYKTSLRNLSACGIKIVCYNFMPVLDWTRTQLDLEMTDGSKALYFNWIDLAIF 141 ******************************************************************** PP TIGR00695 137 elhilkrpdaekdyteeelvraveeasdmseedkarltrniiaglpGaeegekldrikelleaykdid 204 +l+ilkr +ae+dy++ l ra ++s+++e+d a l n++ g+p +e +l+ +++ ++ yk i lcl|FitnessBrowser__Pedo557:CA265_RS07225 142 DLYILKREGAEADYSKSILDRAEAKYSTLTEQDLADLRVNVLMGIPNEKE-IELETLRNSINEYKAIG 208 **********************************************9888.99*************** PP TIGR00695 205 eeklrenlafflkeilpvaeevGvkmaihpddpprpilGlprivstiedmkklveisdspangitlct 272 + l+enl ffl i v G+km+ihpddpp+ ilGlpri st ed++++++ +d ng+ +ct lcl|FitnessBrowser__Pedo557:CA265_RS07225 209 TQGLKENLKFFLSSIAEVCTTEGIKMTIHPDDPPYAILGLPRIASTLEDFNYIIKEVDQAFNGVCFCT 276 ******************************************************************** PP TIGR00695 273 GsyGvradndlvelakqfadriyfahlrsvkreenpktfheaahlekdvdlyevvkavleeehrrkae 340 Gs+G+ n+ +e+ + +r+yfahlr+vk++e++ +f+ea hl +dv++ye++ka+ ee+ r++ lcl|FitnessBrowser__Pedo557:CA265_RS07225 277 GSLGAGMGNNALEIFNAVKERVYFAHLRNVKKDEDG-SFYEADHLGGDVNMYEIMKALSEENALRDKS 343 ************************************.9**********************99888764 PP TIGR00695 341 GkedlipvrpdhGrqllddlkkktnpGysaigrlkGlaelrGlelal 387 ip rpdhG+q+lddl k tnpGysaigrl+GlaelrGle+ + lcl|FitnessBrowser__Pedo557:CA265_RS07225 344 -----IPFRPDHGHQMLDDLAKVTNPGYSAIGRLRGLAELRGLEIGV 385 .....7*************************************9865 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.12 // [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