Align Galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate PP_3601 PP_3601 galactarate dehydratase
Query= reanno::WCS417:GFF829 (517 letters) >FitnessBrowser__Putida:PP_3601 Length = 517 Score = 872 bits (2254), Expect = 0.0 Identities = 433/517 (83%), Positives = 463/517 (89%) Query: 1 MQLIEHADSPRSIRLHERDNVVIVVNDQGVPAGTEFPDGLVTVDFIPQSHKVTLEDIPEG 60 MQLIEH+DSPR +RLH+ DNVV+VVND G+ G F DGL ++ +PQSHKV I +G Sbjct: 1 MQLIEHSDSPRYVRLHDDDNVVVVVNDGGLGEGARFADGLTLIEGVPQSHKVATVSIAKG 60 Query: 61 GQIIRYGQTIGYALAPIPRGSWVQEDQLRMPTAPPLDSLPLSTEVPEAQAPLEGFTFEGY 120 + RYGQ IGYAL + +GSWVQE QL MP AP LDSLP VP+ PLEGFTFEGY Sbjct: 61 EPVRRYGQIIGYALEDLRQGSWVQESQLAMPAAPELDSLPRCDAVPQPLPPLEGFTFEGY 120 Query: 121 RNADGTVGTRNILGITTTVQCVTGVLDHAVKRIKDELLPKYPHVDDVVALTHSYGCGVAI 180 RNADGTVGTRNILGITTTVQCVTGVL+HAVKRI++ELLPKYP+VDDVVA+THSYGCGVAI Sbjct: 121 RNADGTVGTRNILGITTTVQCVTGVLEHAVKRIRNELLPKYPNVDDVVAITHSYGCGVAI 180 Query: 181 TATDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQAGQVMHDNDSSVDLSEPWLYRLQD 240 A DAYIPIRTVRNLARNPNLGGEALVISLGCEKLQA QVMHDND SVDLS+PWLYRLQD Sbjct: 181 NARDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQASQVMHDNDPSVDLSDPWLYRLQD 240 Query: 241 SSHGFTEMIEQIMALAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA 300 +S GF EMIEQIM LAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA Sbjct: 241 ASLGFVEMIEQIMDLAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYA 300 Query: 301 SDLLLRAGATVMFSEVTEVRDAIYLLTSRAENTQVAQELVREMDWYDRYLAKGEADRSAN 360 +DLL+RAGATV+FSEVTEVRDAIY+LTSRAEN VA LVREMDWYDRYL +G ADRSAN Sbjct: 301 ADLLVRAGATVLFSEVTEVRDAIYMLTSRAENQDVADALVREMDWYDRYLQQGAADRSAN 360 Query: 361 TTPGNKKGGLSNIVEKSLGSIVKSGSSAINGVLGPGERFKGKGLIFCATPASDFVCGTLQ 420 TTPGNKKGGLSNIVEKSLGSIVKSGS AI GVLGPGER KGLIFCATPASDFVCGTLQ Sbjct: 361 TTPGNKKGGLSNIVEKSLGSIVKSGSGAIQGVLGPGERANRKGLIFCATPASDFVCGTLQ 420 Query: 421 LAAGMNLHVFTTGRGTPYGLAMAPVVKVSTRTELAQRWPDLIDIDAGRIATGRATIEELG 480 LAAGMNLHVFTTGRGTPYGLAMAPVVKV TR+ELAQRWPDLIDIDAGRIA+GR+TIEELG Sbjct: 421 LAAGMNLHVFTTGRGTPYGLAMAPVVKVCTRSELAQRWPDLIDIDAGRIASGRSTIEELG 480 Query: 481 WELFHFYLDVASGRKQTWAEHHKLHNDITLFNPAPIT 517 WELFH+YLDVASGRKQTWAE H+LHNDITLFNPAPIT Sbjct: 481 WELFHYYLDVASGRKQTWAEQHRLHNDITLFNPAPIT 517 Lambda K H 0.318 0.135 0.401 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: 910 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: 517 Length of database: 517 Length adjustment: 35 Effective length of query: 482 Effective length of database: 482 Effective search space: 232324 Effective search space used: 232324 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 (21.7 bits) S2: 52 (24.6 bits)
Align candidate PP_3601 PP_3601 (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.1949249.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-287 939.6 0.0 2.1e-287 939.4 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_3601 PP_3601 galactarate dehydratase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_3601 PP_3601 galactarate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 939.4 0.0 2.1e-287 2.1e-287 2 507 .] 12 517 .] 11 517 .] 1.00 Alignments for each domain: == domain 1 score: 939.4 bits; conditional E-value: 2.1e-287 TIGR03248 2 yirvneqdnvaivvndkGlpagtefedgltlvekipqghkvalvdlekgdaiirygeviGyavkdiarGswvkee 76 y+r++++dnv++vvnd Gl +g++f+dgltl+e +pq+hkva+v ++kg+ ++ryg++iGya++d+ +Gswv+e+ lcl|FitnessBrowser__Putida:PP_3601 12 YVRLHDDDNVVVVVNDGGLGEGARFADGLTLIEGVPQSHKVATVSIAKGEPVRRYGQIIGYALEDLRQGSWVQES 86 89************************************************************************* PP TIGR03248 77 llelpsapaleelplatkvpeklapleGytfeGyrnadGsvGtknilgittsvqcvagvvdyavkrikkellpky 151 +l +p+ap+l++lp +++vp++l+pleG+tfeGyrnadG+vGt+nilgitt+vqcv+gv+++avkri++ellpky lcl|FitnessBrowser__Putida:PP_3601 87 QLAMPAAPELDSLPRCDAVPQPLPPLEGFTFEGYRNADGTVGTRNILGITTTVQCVTGVLEHAVKRIRNELLPKY 161 *************************************************************************** PP TIGR03248 152 pnvddvvalnhsyGcGvaidapdaivpirtlrnlalnpnlGGealvvglGceklqperllpeelsavelkdaavl 226 pnvddvva++hsyGcGvai+a da++pirt+rnla+npnlGGealv++lGceklq++++++++ +v+l+d++++ lcl|FitnessBrowser__Putida:PP_3601 162 PNVDDVVAITHSYGCGVAINARDAYIPIRTVRNLARNPNLGGEALVISLGCEKLQASQVMHDNDPSVDLSDPWLY 236 *************************************************************************** PP TIGR03248 227 rlqdeklGfaemveailelaeerlkklnarkretvpaselvvGlqcGGsdafsGvtanpavGfaadllvraGatv 301 rlqd++lGf em+e+i++lae+rlkkl++r+retvpasel++G+qcGGsdafsG+tanpa+G+aadllvraGatv lcl|FitnessBrowser__Putida:PP_3601 237 RLQDASLGFVEMIEQIMDLAETRLKKLDQRRRETVPASELILGMQCGGSDAFSGITANPALGYAADLLVRAGATV 311 *************************************************************************** PP TIGR03248 302 lfsevtevrdaihlltpraedaevakaliremkwydeylarGeadrsanttpGnkkGGlsnivekalGsivksGs 376 lfsevtevrdai++lt+rae+++va al+rem+wyd+yl++G adrsanttpGnkkGGlsnivek+lGsivksGs lcl|FitnessBrowser__Putida:PP_3601 312 LFSEVTEVRDAIYMLTSRAENQDVADALVREMDWYDRYLQQGAADRSANTTPGNKKGGLSNIVEKSLGSIVKSGS 386 *************************************************************************** PP TIGR03248 377 saivevlspGekvkkkGliyaatpasdfvcGtlqlasglnlhvfttGrGtpyGlalvpvikvstrtelaerwadl 451 ai++vl+pGe++++kGli++atpasdfvcGtlqla+g+nlhvfttGrGtpyGla++pv+kv+tr+ela+rw dl lcl|FitnessBrowser__Putida:PP_3601 387 GAIQGVLGPGERANRKGLIFCATPASDFVCGTLQLAAGMNLHVFTTGRGTPYGLAMAPVVKVCTRSELAQRWPDL 461 *************************************************************************** PP TIGR03248 452 idldaGriatGeatiedvGwelfrlildvasGrkktwaekyklhndlalfnpapvt 507 id+daGria+G+ tie++Gwelf+ +ldvasGrk+twae+++lhnd++lfnpap+t lcl|FitnessBrowser__Putida:PP_3601 462 IDIDAGRIASGRSTIEELGWELFHYYLDVASGRKQTWAEQHRLHNDITLFNPAPIT 517 *******************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (507 nodes) Target sequences: 1 (517 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: 27.39 // [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