Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate RR42_RS29090 RR42_RS29090 galactarate dehydrogenase
Query= reanno::HerbieS:HSERO_RS15800 (522 letters) >FitnessBrowser__Cup4G11:RR42_RS29090 Length = 512 Score = 820 bits (2118), Expect = 0.0 Identities = 405/508 (79%), Positives = 453/508 (89%), Gaps = 2/508 (0%) Query: 15 YIMMNDTDNVAIVVNDGGLPAGTVFPDGLTLVDRVPQGHKIALRDLKQGEAIVRYDVAIG 74 YI ++ DNVAIV NDGGLP GTVFP GLTL +RVPQGHK+AL DL G+A+VRY+V IG Sbjct: 7 YIRIHALDNVAIVANDGGLPEGTVFPCGLTLRERVPQGHKVALVDLAAGDAVVRYNVVIG 66 Query: 75 YAVRDIPKGGWIEESLVQMPPARELDNLPIATKKPAPQPPLEGYTFEGYRNADGSVGTRN 134 YA+RD+PKG W+ E +++MP A LDNLP+ T+ P PPLEGY+FEG+RN DGSVGTRN Sbjct: 67 YALRDLPKGSWVNERVIEMPVAPGLDNLPVGTRVAEPLPPLEGYSFEGFRNPDGSVGTRN 126 Query: 135 LLAITTTVQCVAGVVEHAVKRIRAELLPKYPNVEDVVALEHTYGCGVAIDAPNAGIPIRT 194 +LAITTTVQCV+GVVEHAV+RIRAELLP+YPNV+DVV LEHTYGCGVAIDAP+A +PIRT Sbjct: 127 ILAITTTVQCVSGVVEHAVRRIRAELLPQYPNVDDVVGLEHTYGCGVAIDAPDAIVPIRT 186 Query: 195 LRNISLNPNFGGQAMVVSLGCEKLQPNRLLPENMIPIHKQGEPYVVCLQDAEHVGFNSMI 254 LRNI+LNPNFGG AM+VSLGCEKLQP RLLP +P + VVCLQD EHVGF SMI Sbjct: 187 LRNIALNPNFGGTAMMVSLGCEKLQPERLLPAGSLPGGL--DVGVVCLQDDEHVGFESMI 244 Query: 255 DSIMNMAEARLTELNKRRRETCPASDLVVGVQCGGSDAFSGVTANPAVGFATDLLVRAGA 314 DSIM MA L L++RRRETCPAS+LVVGVQCGGSDAFSGVTANPAVGFATDLLVRAGA Sbjct: 245 DSIMAMAHTHLARLDQRRRETCPASELVVGVQCGGSDAFSGVTANPAVGFATDLLVRAGA 304 Query: 315 SVMFSEVTEVRDGIDQLTSRAVNEEVAQAMIREMDWYDNYLKQGGVDRSANTTPGNKKGG 374 +VMFSEVTEVRDGIDQLT+RA EVAQAMIREMDWYD YL++G VDRSANTTPGNKKGG Sbjct: 305 TVMFSEVTEVRDGIDQLTARAATPEVAQAMIREMDWYDRYLEKGRVDRSANTTPGNKKGG 364 Query: 375 LANIVEKAMGSIVKSGSSPISGVLSPGDKLQQKGLIYAATPASDFICGTLQLAAGMNLHI 434 L+NIVEKAMGSIVKSGS+ I+GVLSPG+KL+QKGLIYAATPASDFICGTLQLAAGMNLH+ Sbjct: 365 LSNIVEKAMGSIVKSGSTAITGVLSPGEKLKQKGLIYAATPASDFICGTLQLAAGMNLHV 424 Query: 435 FTTGRGTPYGLAAVPVIKVATRNDLARRWHDLMDVNAGRIASGEASIEDVGWELFQLMLD 494 FTTGRGTPYGLA VPVIKVATR+DLARRWHDLMDVNAGRIA+GEA+IEDVGWELF+LMLD Sbjct: 425 FTTGRGTPYGLAEVPVIKVATRSDLARRWHDLMDVNAGRIATGEATIEDVGWELFRLMLD 484 Query: 495 VASGKKRTWAEQWKLHNALTLFNPAPVT 522 VASG+K+TWAE KLHN+L LFNPAPVT Sbjct: 485 VASGRKKTWAEHHKLHNSLVLFNPAPVT 512 Lambda K H 0.317 0.134 0.397 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: 987 Number of extensions: 32 Number of successful extensions: 2 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: 522 Length of database: 512 Length adjustment: 35 Effective length of query: 487 Effective length of database: 477 Effective search space: 232299 Effective search space used: 232299 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 bits)
Align candidate RR42_RS29090 RR42_RS29090 (galactarate dehydrogenase)
to HMM TIGR03248 (garD: galactarate dehydratase (EC 4.2.1.42))
# 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/TIGR03248.hmm # target sequence database: /tmp/gapView.30767.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03248 [M=507] Accession: TIGR03248 Description: galactar-dH20: galactarate 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-292 956.4 0.2 1.6e-292 956.3 0.2 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS29090 RR42_RS29090 galactarate dehydro Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS29090 RR42_RS29090 galactarate dehydrogenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 956.3 0.2 1.6e-292 1.6e-292 1 507 [] 6 512 .] 6 512 .] 1.00 Alignments for each domain: == domain 1 score: 956.3 bits; conditional E-value: 1.6e-292 TIGR03248 1 lyirvneqdnvaivvndkGlpagtefedgltlvekipqghkvalvdlekgdaiirygeviGyavkdiar 69 lyir+++ dnvaiv+nd Glp+gt+f++gltl+e++pqghkvalvdl++gda++ry+ viGya++d+++ lcl|FitnessBrowser__Cup4G11:RR42_RS29090 6 LYIRIHALDNVAIVANDGGLPEGTVFPCGLTLRERVPQGHKVALVDLAAGDAVVRYNVVIGYALRDLPK 74 79******************************************************************* PP TIGR03248 70 GswvkeellelpsapaleelplatkvpeklapleGytfeGyrnadGsvGtknilgittsvqcvagvvdy 138 Gswv+e+++e+p ap l++lp++t+v+e+l+pleGy+feG+rn dGsvGt+nil+itt+vqcv+gvv++ lcl|FitnessBrowser__Cup4G11:RR42_RS29090 75 GSWVNERVIEMPVAPGLDNLPVGTRVAEPLPPLEGYSFEGFRNPDGSVGTRNILAITTTVQCVSGVVEH 143 ********************************************************************* PP TIGR03248 139 avkrikkellpkypnvddvvalnhsyGcGvaidapdaivpirtlrnlalnpnlGGealvvglGceklqp 207 av+ri++ellp+ypnvddvv+l+h+yGcGvaidapdaivpirtlrn+alnpn+GG+a++v+lGceklqp lcl|FitnessBrowser__Cup4G11:RR42_RS29090 144 AVRRIRAELLPQYPNVDDVVGLEHTYGCGVAIDAPDAIVPIRTLRNIALNPNFGGTAMMVSLGCEKLQP 212 ********************************************************************* PP TIGR03248 208 erllpeelsavelkdaavlrlqdekl.GfaemveailelaeerlkklnarkretvpaselvvGlqcGGs 275 erllp + + + d+ v++lqd+++ Gf++m+++i+++a+++l++l++r+ret+paselvvG+qcGGs lcl|FitnessBrowser__Cup4G11:RR42_RS29090 213 ERLLPAGSLP-GGLDVGVVCLQDDEHvGFESMIDSIMAMAHTHLARLDQRRRETCPASELVVGVQCGGS 280 *******999.8889**********99****************************************** PP TIGR03248 276 dafsGvtanpavGfaadllvraGatvlfsevtevrdaihlltpraedaevakaliremkwydeylarGe 344 dafsGvtanpavGfa+dllvraGatv+fsevtevrd+i++lt+ra++ eva+a+irem+wyd+yl++G+ lcl|FitnessBrowser__Cup4G11:RR42_RS29090 281 DAFSGVTANPAVGFATDLLVRAGATVMFSEVTEVRDGIDQLTARAATPEVAQAMIREMDWYDRYLEKGR 349 ********************************************************************* PP TIGR03248 345 adrsanttpGnkkGGlsnivekalGsivksGssaivevlspGekvkkkGliyaatpasdfvcGtlqlas 413 +drsanttpGnkkGGlsniveka+GsivksGs+ai++vlspGek k+kGliyaatpasdf+cGtlqla+ lcl|FitnessBrowser__Cup4G11:RR42_RS29090 350 VDRSANTTPGNKKGGLSNIVEKAMGSIVKSGSTAITGVLSPGEKLKQKGLIYAATPASDFICGTLQLAA 418 ********************************************************************* PP TIGR03248 414 glnlhvfttGrGtpyGlalvpvikvstrtelaerwadlidldaGriatGeatiedvGwelfrlildvas 482 g+nlhvfttGrGtpyGla+vpvikv+tr++la+rw+dl+d++aGriatGeatiedvGwelfrl+ldvas lcl|FitnessBrowser__Cup4G11:RR42_RS29090 419 GMNLHVFTTGRGTPYGLAEVPVIKVATRSDLARRWHDLMDVNAGRIATGEATIEDVGWELFRLMLDVAS 487 ********************************************************************* PP TIGR03248 483 Grkktwaekyklhndlalfnpapvt 507 Grkktwae++klhn+l lfnpapvt lcl|FitnessBrowser__Cup4G11:RR42_RS29090 488 GRKKTWAEHHKLHNSLVLFNPAPVT 512 ************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (507 nodes) Target sequences: 1 (512 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 0.02s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 7.11 // [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