Align D-mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate WP_041741979.1 CALKRO_RS09060 mannonate dehydratase
Query= metacyc::MONOMER-17955 (360 letters) >NCBI__GCF_000166775.1:WP_041741979.1 Length = 359 Score = 582 bits (1499), Expect = e-171 Identities = 263/355 (74%), Positives = 312/355 (87%) Query: 3 LVFRWYGEKHDTVTLEQIRQIPGVEGVVGALFDIPVGEVWPFEEIMKLKETVEKAGLKLE 62 + FRW+G K D + LE IRQIPG+ GVV ALFDIPVGEVWP + I +LK+ VE AGLK E Sbjct: 1 MTFRWFGPKDDNIPLEYIRQIPGIYGVVTALFDIPVGEVWPEDRIFELKKLVEGAGLKFE 60 Query: 63 VIESVNVHEDIKLGLPTRDRYIENYKKTIRNLAKAGVKVVCYNFMPVFDWMRTDLHKKLP 122 VIESVNVHEDIKLGLP+RDRYIENYK+TIRNLAKAGVKV+CYNFMPVFDW+RTDL KKLP Sbjct: 61 VIESVNVHEDIKLGLPSRDRYIENYKQTIRNLAKAGVKVICYNFMPVFDWLRTDLAKKLP 120 Query: 123 DGSETMEYDHRLIEGVTPDELIKRVKEGSQGFVLPGWEWDRLEKLRETFELYKNVDEEKL 182 DGSE MEY+H +++ +TPDEL+K ++ GSQGF LPGWE RL++L+ FE+YK+VDE KL Sbjct: 121 DGSEVMEYNHEILKNMTPDELVKSMERGSQGFSLPGWENYRLKQLQSLFEMYKDVDENKL 180 Query: 183 FENLVYFLERVIPVCEECDVKLAIHPDDPPWSIFGLPRIITNKENIERMLKAVDSPYNGI 242 +NL+YFLE +IPVCE+CDVK+AIHPDDPPWS+FGLPR++TNK+NIE+ LKAVDSPYNG+ Sbjct: 181 LQNLIYFLENIIPVCEQCDVKMAIHPDDPPWSLFGLPRVVTNKKNIEKFLKAVDSPYNGL 240 Query: 243 TFCMGSLGANPENNIPEMIRYFGKMGRIHFAHVRNLKFTGEKSFYETAHPSFCGSHDLFE 302 T C GSLGAN ENNIPE+IRYFGKMGRIHF HVRN+KFTGE+SFYET+H S GS D+FE Sbjct: 241 TLCTGSLGANRENNIPELIRYFGKMGRIHFMHVRNIKFTGERSFYETSHLSTDGSFDMFE 300 Query: 303 VMKAFHDIGYEGYIRPDHGRLIWGEKARPGYGLYDRALGATYILGLWEAIDKMKK 357 ++KA +DIG++GY+RPDHGR+IWGEK RPGYGLYDRALG Y+ GLWEAIDKM + Sbjct: 301 IIKAIYDIGFDGYLRPDHGRMIWGEKGRPGYGLYDRALGIAYLNGLWEAIDKMSR 355 Lambda K H 0.322 0.142 0.448 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: 551 Number of extensions: 20 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: 360 Length of database: 359 Length adjustment: 29 Effective length of query: 331 Effective length of database: 330 Effective search space: 109230 Effective search space used: 109230 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: 49 (23.5 bits)
Align candidate WP_041741979.1 CALKRO_RS09060 (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.569895.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-128 413.2 0.0 5.7e-126 406.7 0.0 2.0 1 NCBI__GCF_000166775.1:WP_041741979.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166775.1:WP_041741979.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 406.7 0.0 5.7e-126 5.7e-126 3 392 .. 1 355 [. 1 357 [. 0.95 Alignments for each domain: == domain 1 score: 406.7 bits; conditional E-value: 5.7e-126 TIGR00695 3 qtfrwyGr.ndpvsledvrqa.GakGivtalhhipnGevweveeikkrkeeiedaGlsasvvesvpvheeikl 73 +tfrw+G+ +d + le++rq+ G+ G+vtal +ip+Gevw + i + k+ +e aGl+++v+esv+vhe+ikl NCBI__GCF_000166775.1:WP_041741979.1 1 MTFRWFGPkDDNIPLEYIRQIpGIYGVVTALFDIPVGEVWPEDRIFELKKLVEGAGLKFEVIESVNVHEDIKL 73 79******7789************************************************************* PP TIGR00695 74 qteeyekyienykqtlrnlaqcGikvvcynfmpvldwtrtdlayeledGskalrfdkikvaalelhilkrpda 146 + +++yienykqt+rnla+ G+kv+cynfmpv+dw rtdla++l+dGs+ + +++ ++ + p NCBI__GCF_000166775.1:WP_041741979.1 74 GLPSRDRYIENYKQTIRNLAKAGVKVICYNFMPVFDWLRTDLAKKLPDGSEVMEYNHEILKNMT------P-- 138 *****************************************************99986666655......6.. PP TIGR00695 147 ekdyteeelvraveeasdmseedkarltrniiaglpGaeegekldrikelleaykdideeklrenlafflkei 219 +elv+++e+ s+ lpG+e+ ++l++++ l+e+ykd+de+kl +nl +fl++i NCBI__GCF_000166775.1:WP_041741979.1 139 ------DELVKSMERGSQGF-------------SLPGWEN-YRLKQLQSLFEMYKDVDENKLLQNLIYFLENI 191 ......9******9988765.............6******.******************************** PP TIGR00695 220 lpvaeevGvkmaihpddpprpilGlprivstiedmkklveisdspangitlctGsyGvradndlvelakqfa. 291 +pv e+ vkmaihpddpp+ ++Glpr+v+ +++++k+ + +dsp ng+tlctGs+G++ +n++ el++ f+ NCBI__GCF_000166775.1:WP_041741979.1 192 IPVCEQCDVKMAIHPDDPPWSLFGLPRVVTNKKNIEKFLKAVDSPYNGLTLCTGSLGANRENNIPELIRYFGk 264 ***********************************************************************84 PP TIGR00695 292 .driyfahlrsvkreenpktfheaahlekdv..dlyevvkavleeehrrkaeGkedlipvrpdhGrqllddlk 361 +ri+f h+r++k ++ +f+e++hl+ d+ d++e++ka+ + +G + +rpdhGr +++ NCBI__GCF_000166775.1:WP_041741979.1 265 mGRIHFMHVRNIKFTGER-SFYETSHLSTDGsfDMFEIIKAIYDI----GFDG----Y-LRPDHGRMIWG--- 324 459***********9987.9*******999844799999998665....5678....6.9**********... PP TIGR00695 362 kktnpGysaigrlkGlaelrGlelalkkvaf 392 +k +pGy++++r++G+a+l+Gl+ a++k+ NCBI__GCF_000166775.1:WP_041741979.1 325 EKGRPGYGLYDRALGIAYLNGLWEAIDKMSR 355 9**************************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (394 nodes) Target sequences: 1 (359 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: 00:00:00.01 # Mc/sec: 13.59 // [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