Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate HSERO_RS15800 HSERO_RS15800 D-galactarate dehydratase
Query= reanno::HerbieS:HSERO_RS15800 (522 letters) >FitnessBrowser__HerbieS:HSERO_RS15800 Length = 522 Score = 1044 bits (2699), Expect = 0.0 Identities = 522/522 (100%), Positives = 522/522 (100%) Query: 1 MSTDTSASQASAPRYIMMNDTDNVAIVVNDGGLPAGTVFPDGLTLVDRVPQGHKIALRDL 60 MSTDTSASQASAPRYIMMNDTDNVAIVVNDGGLPAGTVFPDGLTLVDRVPQGHKIALRDL Sbjct: 1 MSTDTSASQASAPRYIMMNDTDNVAIVVNDGGLPAGTVFPDGLTLVDRVPQGHKIALRDL 60 Query: 61 KQGEAIVRYDVAIGYAVRDIPKGGWIEESLVQMPPARELDNLPIATKKPAPQPPLEGYTF 120 KQGEAIVRYDVAIGYAVRDIPKGGWIEESLVQMPPARELDNLPIATKKPAPQPPLEGYTF Sbjct: 61 KQGEAIVRYDVAIGYAVRDIPKGGWIEESLVQMPPARELDNLPIATKKPAPQPPLEGYTF 120 Query: 121 EGYRNADGSVGTRNLLAITTTVQCVAGVVEHAVKRIRAELLPKYPNVEDVVALEHTYGCG 180 EGYRNADGSVGTRNLLAITTTVQCVAGVVEHAVKRIRAELLPKYPNVEDVVALEHTYGCG Sbjct: 121 EGYRNADGSVGTRNLLAITTTVQCVAGVVEHAVKRIRAELLPKYPNVEDVVALEHTYGCG 180 Query: 181 VAIDAPNAGIPIRTLRNISLNPNFGGQAMVVSLGCEKLQPNRLLPENMIPIHKQGEPYVV 240 VAIDAPNAGIPIRTLRNISLNPNFGGQAMVVSLGCEKLQPNRLLPENMIPIHKQGEPYVV Sbjct: 181 VAIDAPNAGIPIRTLRNISLNPNFGGQAMVVSLGCEKLQPNRLLPENMIPIHKQGEPYVV 240 Query: 241 CLQDAEHVGFNSMIDSIMNMAEARLTELNKRRRETCPASDLVVGVQCGGSDAFSGVTANP 300 CLQDAEHVGFNSMIDSIMNMAEARLTELNKRRRETCPASDLVVGVQCGGSDAFSGVTANP Sbjct: 241 CLQDAEHVGFNSMIDSIMNMAEARLTELNKRRRETCPASDLVVGVQCGGSDAFSGVTANP 300 Query: 301 AVGFATDLLVRAGASVMFSEVTEVRDGIDQLTSRAVNEEVAQAMIREMDWYDNYLKQGGV 360 AVGFATDLLVRAGASVMFSEVTEVRDGIDQLTSRAVNEEVAQAMIREMDWYDNYLKQGGV Sbjct: 301 AVGFATDLLVRAGASVMFSEVTEVRDGIDQLTSRAVNEEVAQAMIREMDWYDNYLKQGGV 360 Query: 361 DRSANTTPGNKKGGLANIVEKAMGSIVKSGSSPISGVLSPGDKLQQKGLIYAATPASDFI 420 DRSANTTPGNKKGGLANIVEKAMGSIVKSGSSPISGVLSPGDKLQQKGLIYAATPASDFI Sbjct: 361 DRSANTTPGNKKGGLANIVEKAMGSIVKSGSSPISGVLSPGDKLQQKGLIYAATPASDFI 420 Query: 421 CGTLQLAAGMNLHIFTTGRGTPYGLAAVPVIKVATRNDLARRWHDLMDVNAGRIASGEAS 480 CGTLQLAAGMNLHIFTTGRGTPYGLAAVPVIKVATRNDLARRWHDLMDVNAGRIASGEAS Sbjct: 421 CGTLQLAAGMNLHIFTTGRGTPYGLAAVPVIKVATRNDLARRWHDLMDVNAGRIASGEAS 480 Query: 481 IEDVGWELFQLMLDVASGKKRTWAEQWKLHNALTLFNPAPVT 522 IEDVGWELFQLMLDVASGKKRTWAEQWKLHNALTLFNPAPVT Sbjct: 481 IEDVGWELFQLMLDVASGKKRTWAEQWKLHNALTLFNPAPVT 522 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: 1110 Number of extensions: 35 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: 522 Length of database: 522 Length adjustment: 35 Effective length of query: 487 Effective length of database: 487 Effective search space: 237169 Effective search space used: 237169 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 HSERO_RS15800 HSERO_RS15800 (D-galactarate dehydratase)
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.31090.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.2e-290 947.4 0.2 9.2e-290 947.2 0.2 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS15800 HSERO_RS15800 D-galactarate dehy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS15800 HSERO_RS15800 D-galactarate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 947.2 0.2 9.2e-290 9.2e-290 2 507 .] 15 522 .] 14 522 .] 0.99 Alignments for each domain: == domain 1 score: 947.2 bits; conditional E-value: 9.2e-290 TIGR03248 2 yirvneqdnvaivvndkGlpagtefedgltlvekipqghkvalvdlekgdaiirygeviGyavkdiar 69 yi +n++dnvaivvnd Glpagt+f+dgltlv+++pqghk+al dl++g+ai+ry+ iGyav+di++ lcl|FitnessBrowser__HerbieS:HSERO_RS15800 15 YIMMNDTDNVAIVVNDGGLPAGTVFPDGLTLVDRVPQGHKIALRDLKQGEAIVRYDVAIGYAVRDIPK 82 899***************************************************************** PP TIGR03248 70 GswvkeellelpsapaleelplatkvpeklapleGytfeGyrnadGsvGtknilgittsvqcvagvvd 137 G w++e+l+++p a +l++lp+atk+p++++pleGytfeGyrnadGsvGt+n+l+itt+vqcvagvv+ lcl|FitnessBrowser__HerbieS:HSERO_RS15800 83 GGWIEESLVQMPPARELDNLPIATKKPAPQPPLEGYTFEGYRNADGSVGTRNLLAITTTVQCVAGVVE 150 ******************************************************************** PP TIGR03248 138 yavkrikkellpkypnvddvvalnhsyGcGvaidapdaivpirtlrnlalnpnlGGealvvglGcekl 205 +avkri++ellpkypnv+dvval+h+yGcGvaidap+a +pirtlrn++lnpn+GG+a+vv+lGcekl lcl|FitnessBrowser__HerbieS:HSERO_RS15800 151 HAVKRIRAELLPKYPNVEDVVALEHTYGCGVAIDAPNAGIPIRTLRNISLNPNFGGQAMVVSLGCEKL 218 ******************************************************************** PP TIGR03248 206 qperllpeelsave.lkdaavlrlqdekl.GfaemveailelaeerlkklnarkretvpaselvvGlq 271 qp+rllpe++++++ + ++ v++lqd+++ Gf++m+++i+++ae rl++ln+r+ret+pas+lvvG+q lcl|FitnessBrowser__HerbieS:HSERO_RS15800 219 QPNRLLPENMIPIHkQGEPYVVCLQDAEHvGFNSMIDSIMNMAEARLTELNKRRRETCPASDLVVGVQ 286 **********9976156999********99************************************** PP TIGR03248 272 cGGsdafsGvtanpavGfaadllvraGatvlfsevtevrdaihlltpraedaevakaliremkwydey 339 cGGsdafsGvtanpavGfa+dllvraGa+v+fsevtevrd+i++lt+ra ++eva+a+irem+wyd+y lcl|FitnessBrowser__HerbieS:HSERO_RS15800 287 CGGSDAFSGVTANPAVGFATDLLVRAGASVMFSEVTEVRDGIDQLTSRAVNEEVAQAMIREMDWYDNY 354 ******************************************************************** PP TIGR03248 340 larGeadrsanttpGnkkGGlsnivekalGsivksGssaivevlspGekvkkkGliyaatpasdfvcG 407 l++G +drsanttpGnkkGGl+niveka+GsivksGss+i++vlspG+k ++kGliyaatpasdf+cG lcl|FitnessBrowser__HerbieS:HSERO_RS15800 355 LKQGGVDRSANTTPGNKKGGLANIVEKAMGSIVKSGSSPISGVLSPGDKLQQKGLIYAATPASDFICG 422 ******************************************************************** PP TIGR03248 408 tlqlasglnlhvfttGrGtpyGlalvpvikvstrtelaerwadlidldaGriatGeatiedvGwelfr 475 tlqla+g+nlh+fttGrGtpyGla+vpvikv+tr++la+rw+dl+d++aGria+Gea+iedvGwelf+ lcl|FitnessBrowser__HerbieS:HSERO_RS15800 423 TLQLAAGMNLHIFTTGRGTPYGLAAVPVIKVATRNDLARRWHDLMDVNAGRIASGEASIEDVGWELFQ 490 ******************************************************************** PP TIGR03248 476 lildvasGrkktwaekyklhndlalfnpapvt 507 l+ldvasG+k+twae++klhn+l+lfnpapvt lcl|FitnessBrowser__HerbieS:HSERO_RS15800 491 LMLDVASGKKRTWAEQWKLHNALTLFNPAPVT 522 *******************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (507 nodes) Target sequences: 1 (522 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 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 8.78 // [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