Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate WP_007675859.1 BN137_RS06950 mannonate dehydratase
Query= BRENDA::P24215 (394 letters) >NCBI__GCF_000319285.1:WP_007675859.1 Length = 396 Score = 617 bits (1590), Expect = 0.0 Identities = 299/392 (76%), Positives = 330/392 (84%) Query: 1 MEQTWRWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWS 60 MEQTWRWYGPNDPVSL D+RQAGATG+VTALHHIPNGEVW VEEI KR+A + GL WS Sbjct: 1 MEQTWRWYGPNDPVSLDDIRQAGATGIVTALHHIPNGEVWPVEEIKKRQAELAQKGLTWS 60 Query: 61 VVESVPIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLP 120 VVES+P+HEDIKTHTG Y+ +IA YQQ++RNLA CGI TVCYNFMP+LDWTRTDLEY LP Sbjct: 61 VVESIPVHEDIKTHTGEYDLYIARYQQSIRNLAVCGIDTVCYNFMPILDWTRTDLEYTLP 120 Query: 121 DGSKALRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAG 180 DGSKALRFDQI FAAFE+HILKR GA DYTE+E QA + F MS+ LTRNIIAG Sbjct: 121 DGSKALRFDQIAFAAFELHILKRDGARNDYTEDEQRQAQDYFHAMSEAQIETLTRNIIAG 180 Query: 181 LPGAEEGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRP 240 LPGAEEGYTLDQFR L Y IDKA LREN A FLKAI+PVAEE GVR+AVHPDDPPRP Sbjct: 181 LPGAEEGYTLDQFRARLAEYDPIDKAALRENMAYFLKAIVPVAEEAGVRLAVHPDDPPRP 240 Query: 241 ILGLPRIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLR 300 ILGLPRIVSTIEDM W+ +TV+S+ NGFTMCTGSYGVRADNDLV M++ F RI+FTHLR Sbjct: 241 ILGLPRIVSTIEDMLWLKETVDSIYNGFTMCTGSYGVRADNDLVRMVETFADRIHFTHLR 300 Query: 301 STMREDNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDL 360 +T RE NPKTFHEAAHL GDVDM VVKAI+ EE RRK G IP RPDHGHQMLDDL Sbjct: 301 ATCREANPKTFHEAAHLYGDVDMVAVVKAILTEEQRRKKAGDLRPIPFRPDHGHQMLDDL 360 Query: 361 KKKTNPGYSAIGRLKGLAEVRGVELAIQRAFF 392 +KKTNPGYSAIGRLKGLAEVRG+ELA+++ F Sbjct: 361 RKKTNPGYSAIGRLKGLAEVRGIELALKKVLF 392 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: 594 Number of extensions: 22 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: 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_007675859.1 BN137_RS06950 (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.3410037.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-210 682.8 0.0 8.9e-210 682.6 0.0 1.0 1 NCBI__GCF_000319285.1:WP_007675859.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000319285.1:WP_007675859.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 682.6 0.0 8.9e-210 8.9e-210 1 392 [. 1 392 [. 1 394 [. 1.00 Alignments for each domain: == domain 1 score: 682.6 bits; conditional E-value: 8.9e-210 TIGR00695 1 meqtfrwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheeikl 73 meqt+rwyG+ndpvsl+d+rqaGa+GivtalhhipnGevw veeikkr++e+ + Gl++svves+pvhe+ik+ NCBI__GCF_000319285.1:WP_007675859.1 1 MEQTWRWYGPNDPVSLDDIRQAGATGIVTALHHIPNGEVWPVEEIKKRQAELAQKGLTWSVVESIPVHEDIKT 73 9************************************************************************ PP TIGR00695 74 qteeyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalelhilkrpda 146 +t+ey+ yi+ y+q++rnla cGi++vcynfmp+ldwtrtdl+y+l+dGskalrfd+i++aa+elhilkr +a NCBI__GCF_000319285.1:WP_007675859.1 74 HTGEYDLYIARYQQSIRNLAVCGIDTVCYNFMPILDWTRTDLEYTLPDGSKALRFDQIAFAAFELHILKRDGA 146 ************************************************************************* PP TIGR00695 147 ekdyteeelvraveeasdmseedkarltrniiaglpGaeegekldrikelleaykdideeklrenlafflkei 219 +dyte+e+ +a+++++ mse ++ ltrniiaglpGaeeg++ld+++ +l+ y id++ lren+a+flk+i NCBI__GCF_000319285.1:WP_007675859.1 147 RNDYTEDEQRQAQDYFHAMSEAQIETLTRNIIAGLPGAEEGYTLDQFRARLAEYDPIDKAALRENMAYFLKAI 219 ************************************************************************* PP TIGR00695 220 lpvaeevGvkmaihpddpprpilGlprivstiedmkklveisdspangitlctGsyGvradndlvelakqfad 292 +pvaee Gv++a+hpddpprpilGlprivstiedm +l+e++ds ng+t+ctGsyGvradndlv ++++fad NCBI__GCF_000319285.1:WP_007675859.1 220 VPVAEEAGVRLAVHPDDPPRPILGLPRIVSTIEDMLWLKETVDSIYNGFTMCTGSYGVRADNDLVRMVETFAD 292 ************************************************************************* PP TIGR00695 293 riyfahlrsvkreenpktfheaahlekdvdlyevvkavleeehrrkaeGkedlipvrpdhGrqllddlkkktn 365 ri+f+hlr++ re npktfheaahl +dvd+ vvka+l ee rrk+ G+ + ip rpdhG+q+lddl+kktn NCBI__GCF_000319285.1:WP_007675859.1 293 RIHFTHLRATCREANPKTFHEAAHLYGDVDMVAVVKAILTEEQRRKKAGDLRPIPFRPDHGHQMLDDLRKKTN 365 ************************************************************************* PP TIGR00695 366 pGysaigrlkGlaelrGlelalkkvaf 392 pGysaigrlkGlae+rG+elalkkv f NCBI__GCF_000319285.1:WP_007675859.1 366 PGYSAIGRLKGLAEVRGIELALKKVLF 392 ************************987 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 20.86 // [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