Align mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate Echvi_3100 Echvi_3100 mannonate dehydratase
Query= BRENDA::P24215 (394 letters) >FitnessBrowser__Cola:Echvi_3100 Length = 382 Score = 467 bits (1201), Expect = e-136 Identities = 227/382 (59%), Positives = 291/382 (76%), Gaps = 6/382 (1%) Query: 6 RWYGPNDPVSLADVRQAGATGVVTALHHIPNGEVWSVEEILKRKAIIEDAGLVWSVVESV 65 RWYGP DPV+LAD+RQAGATG+V+ALHH+PNG +WS EEI KRK IE AGL WSVVES+ Sbjct: 2 RWYGPQDPVTLADIRQAGATGIVSALHHLPNGVIWSREEIKKRKDTIEAAGLTWSVVESI 61 Query: 66 PIHEDIKTHTGNYEQWIANYQQTLRNLAQCGIRTVCYNFMPVLDWTRTDLEYVLPDGSKA 125 P+HE+IKT +GNY+++IANY+ ++ NLA GI TVCYNFMPVLDWTRTDL Y LP+G+KA Sbjct: 62 PVHENIKTRSGNYQEYIANYKTSIGNLAAEGIHTVCYNFMPVLDWTRTDLAYELPNGAKA 121 Query: 126 LRFDQIEFAAFEMHILKRPGAEADYTEEEIAQAAERFATMSDEDKARLTRNIIAGLPGAE 185 LRF+ AAF++ IL+RP AE DY+E+ I +A F M+++ + LT NIIAGLPGAE Sbjct: 122 LRFELQALAAFDLFILQRPNAEKDYSEQVIKRAEAYFKEMTEDAEQLLTNNIIAGLPGAE 181 Query: 186 EGYTLDQFRKHLELYKDIDKAKLRENFAVFLKAIIPVAEEVGVRMAVHPDDPPRPILGLP 245 EGY+L F++ L+ Y+ ID KL N +FL+ IIP AE+ V MA+HPDDPP P+ GLP Sbjct: 182 EGYSLKAFQQVLDTYQHIDADKLATNLRLFLEEIIPTAEKNRVFMAIHPDDPPFPMFGLP 241 Query: 246 RIVSTIEDMQWMVDTVNSMANGFTMCTGSYGVRADNDLVDMIKQFGPRIYFTHLRSTMRE 305 R++STI+D++ +V S NG T CTGS+GVRADNDL +I++ G I+F HLRST R Sbjct: 242 RVMSTIDDVKRLVTETPSEYNGITFCTGSFGVRADNDLPQIIREHGDHIHFIHLRSTQR- 300 Query: 306 DNPKTFHEAAHLNGDVDMYEVVKAIVEEEHRRKAEGKEDLIPMRPDHGHQMLDDLKKKTN 365 D FHEA HL GDV + V+K +++ + RR+ +PMRPDHGHQMLDDL+K TN Sbjct: 301 DAYGNFHEANHLEGDVPIVAVIKELIKVQSRRQKS-----LPMRPDHGHQMLDDLRKTTN 355 Query: 366 PGYSAIGRLKGLAEVRGVELAI 387 PGY+ IGRLKGLAE+RG+E+ + Sbjct: 356 PGYTGIGRLKGLAELRGLEMGL 377 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: 510 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: 382 Length adjustment: 30 Effective length of query: 364 Effective length of database: 352 Effective search space: 128128 Effective search space used: 128128 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 Echvi_3100 Echvi_3100 (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.28475.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-171 554.9 0.0 6.7e-171 554.6 0.0 1.0 1 lcl|FitnessBrowser__Cola:Echvi_3100 Echvi_3100 mannonate dehydratase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_3100 Echvi_3100 mannonate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 554.6 0.0 6.7e-171 6.7e-171 6 387 .. 2 377 .. 1 380 [. 0.98 Alignments for each domain: == domain 1 score: 554.6 bits; conditional E-value: 6.7e-171 TIGR00695 6 rwyGrndpvsledvrqaGakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheeiklqteeye 79 rwyG++dpv+l+d+rqaGa+Giv alhh pnG +w+ eeikkrk++ie aGl++svves+pvhe+ik+++++y+ lcl|FitnessBrowser__Cola:Echvi_3100 2 RWYGPQDPVTLADIRQAGATGIVSALHHLPNGVIWSREEIKKRKDTIEAAGLTWSVVESIPVHENIKTRSGNYQ 75 9************************************************************************* PP TIGR00695 80 kyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalelhilkrpdaekdytee 153 +yi+nyk ++ nla Gi++vcynfmpvldwtrtdlayel++G+kalrf+ ++aa++l+il+rp+aekdy+e+ lcl|FitnessBrowser__Cola:Echvi_3100 76 EYIANYKTSIGNLAAEGIHTVCYNFMPVLDWTRTDLAYELPNGAKALRFELQALAAFDLFILQRPNAEKDYSEQ 149 ************************************************************************** PP TIGR00695 154 elvraveeasdmseedkarltrniiaglpGaeegekldrikelleaykdideeklrenlafflkeilpvaeevG 227 + ra ++++m+e+ lt niiaglpGaeeg+ l+ +++ l++y+ id +kl +nl +fl+ei+p ae+ lcl|FitnessBrowser__Cola:Echvi_3100 150 VIKRAEAYFKEMTEDAEQLLTNNIIAGLPGAEEGYSLKAFQQVLDTYQHIDADKLATNLRLFLEEIIPTAEKNR 223 *************9999999****************************************************** PP TIGR00695 228 vkmaihpddpprpilGlprivstiedmkklveisdspangitlctGsyGvradndlvelakqfadriyfahlrs 301 v maihpddpp p++Glpr++sti+d+k+lv ++s ngit+ctGs+Gvradndl +++++++d i+f hlrs lcl|FitnessBrowser__Cola:Echvi_3100 224 VFMAIHPDDPPFPMFGLPRVMSTIDDVKRLVTETPSEYNGITFCTGSFGVRADNDLPQIIREHGDHIHFIHLRS 297 ************************************************************************** PP TIGR00695 302 vkreenpktfheaahlekdvdlyevvkavleeehrrkaeGkedlipvrpdhGrqllddlkkktnpGysaigrlk 375 ++r+ + +fhea hle+dv + v+k +++ + rr++ +p+rpdhG+q+lddl+k tnpGy+ igrlk lcl|FitnessBrowser__Cola:Echvi_3100 298 TQRDAYG-NFHEANHLEGDVPIVAVIKELIKVQSRRQKS-----LPMRPDHGHQMLDDLRKTTNPGYTGIGRLK 365 ******9.***************9999999988888765.....5***************************** PP TIGR00695 376 GlaelrGlelal 387 GlaelrGle+ l lcl|FitnessBrowser__Cola:Echvi_3100 366 GLAELRGLEMGL 377 *********975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (382 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 7.35 // [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