Align Glucarate dehydratase; GDH; GlucD; EC 4.2.1.40 (characterized)
to candidate PfGW456L13_2480 Glucarate dehydratase (EC 4.2.1.40)
Query= SwissProt::P42206 (451 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2480 Length = 447 Score = 748 bits (1930), Expect = 0.0 Identities = 356/444 (80%), Positives = 399/444 (89%) Query: 8 QAATGAPVITDLKVVPVAGHDSMLLNLSGAHGPLFTRNILILTDSSGHVGVGEVPGGEGI 67 Q APVIT ++VVPVAGHD MLLNLSGAHGP FTRNI+IL D++GH GVGEVPGGE I Sbjct: 4 QDTAKAPVITSMQVVPVAGHDGMLLNLSGAHGPFFTRNIVILKDNAGHTGVGEVPGGERI 63 Query: 68 RKTLEDARHLLINQSIGNYQSLLNKVRNAFADRDVGGRGLQTFDLRIAVHAVTAVESALL 127 R+TLEDAR L++ IG YQ +LN+VR FADRD GGRGLQTFDLRI +HAVT +E+ALL Sbjct: 64 RQTLEDARSLVVGSPIGTYQKILNQVRQTFADRDAGGRGLQTFDLRITIHAVTGLEAALL 123 Query: 128 DLLGQHLQVPVAALLGEGQQRDAVEMLGYLFYVGDRNKTDLGYRSEHEADNEWFRLRNKE 187 DLLGQHL VPVAALLGEGQQRD V+MLGYLFYVGDRN+TDL YRSE +ADN+WFR+R+++ Sbjct: 124 DLLGQHLDVPVAALLGEGQQRDEVKMLGYLFYVGDRNETDLAYRSEPDADNDWFRVRHEK 183 Query: 188 ALTPESVVALAEAAYDRYGFKDFKLKGGVLRGEDEIAAVTALSERFPDARITLDPNGAWS 247 A+T ++VV LAEAA+ RYGFKDFKLKGGVL G+ EI AVTAL+ERFPDARITLDPNGAWS Sbjct: 184 AMTADAVVRLAEAAHARYGFKDFKLKGGVLSGDAEIEAVTALAERFPDARITLDPNGAWS 243 Query: 248 LKEAVALCRDQHHVLAYAEDPCGAENGYSGREVMAEFRRSTGLRTATNMIATDWRQMGHA 307 LKEA+ LCRDQH VLAYAEDPCGAENGYSGREVMAEFRR+TGL+TATNMIATDWR+MGHA Sbjct: 244 LKEAIRLCRDQHRVLAYAEDPCGAENGYSGREVMAEFRRATGLKTATNMIATDWREMGHA 303 Query: 308 IQLQSVDIPLADPHFWTMQGSVRVAQMCNEWGLTWGSHSNNHFDISLAMFTHVAAAAPGN 367 IQLQSVDIPLADPHFWTMQGSVRVAQMC+EWGLTWGSHSNNHFDISLAMFTHVAAAAPG Sbjct: 304 IQLQSVDIPLADPHFWTMQGSVRVAQMCHEWGLTWGSHSNNHFDISLAMFTHVAAAAPGE 363 Query: 368 ITAIDTHWIWQDGQRLTKEPLQIKGGLVEVPKKPGLGVELDWDALMKAHEVYKSMGLGAR 427 ITAIDTHWIWQDGQRLTK PLQI G V+VP+KPGLGVELD D + KAHE+YK MGLGAR Sbjct: 364 ITAIDTHWIWQDGQRLTKAPLQIVDGCVQVPQKPGLGVELDMDQVAKAHELYKGMGLGAR 423 Query: 428 DDATAMRYLVSGWEFNNKRPCMVR 451 DD+ AM++L+ W+F+NKRPC+VR Sbjct: 424 DDSVAMQFLIPDWKFDNKRPCLVR 447 Lambda K H 0.319 0.135 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: 697 Number of extensions: 15 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: 451 Length of database: 447 Length adjustment: 33 Effective length of query: 418 Effective length of database: 414 Effective search space: 173052 Effective search space used: 173052 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: 51 (24.3 bits)
Align candidate PfGW456L13_2480 (Glucarate dehydratase (EC 4.2.1.40))
to HMM TIGR03247 (gudD: glucarate dehydratase (EC 4.2.1.40))
# 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/TIGR03247.hmm # target sequence database: /tmp/gapView.28337.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03247 [M=441] Accession: TIGR03247 Description: glucar-dehydr: glucarate 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-272 890.3 1.0 1.2e-272 890.1 1.0 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2480 Glucarate dehydratase (EC 4.2.1. Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2480 Glucarate dehydratase (EC 4.2.1.40) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 890.1 1.0 1.2e-272 1.2e-272 2 441 .] 8 447 .] 7 447 .] 1.00 Alignments for each domain: == domain 1 score: 890.1 bits; conditional E-value: 1.2e-272 TIGR03247 2 atpvvtelrvvpvagrdsmllnlsgahapfftrnivilkdssgrtgvgevpggek 56 ++pv+t+++vvpvag+d mllnlsgah+pfftrnivilkd++g+tgvgevpgge+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2480 8 KAPVITSMQVVPVAGHDGMLLNLSGAHGPFFTRNIVILKDNAGHTGVGEVPGGER 62 689**************************************************** PP TIGR03247 57 irktledakalvvgktlgeyknvlkkvrktfadrdaggrgkqtfdlrvtvhavta 111 ir+tleda++lvvg ++g+y+++l++vr+tfadrdaggrg+qtfdlr+t+havt+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2480 63 IRQTLEDARSLVVGSPIGTYQKILNQVRQTFADRDAGGRGLQTFDLRITIHAVTG 117 ******************************************************* PP TIGR03247 112 lesalldllgqhlevpvaallgegqqrdevevlgylffvgdrkktsldyrseeea 166 le+alldllgqhl+vpvaallgegqqrdev++lgylf+vgdr++t+l+yrse++a lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2480 118 LEAALLDLLGQHLDVPVAALLGEGQQRDEVKMLGYLFYVGDRNETDLAYRSEPDA 172 ******************************************************* PP TIGR03247 167 kddwlrlrheealtpeavvrlaeaakdrygfkdfklkggvlrgeeeieavtalak 221 ++dw+r+rhe+a+t +avvrlaeaa++rygfkdfklkggvl+g+ eieavtala+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2480 173 DNDWFRVRHEKAMTADAVVRLAEAAHARYGFKDFKLKGGVLSGDAEIEAVTALAE 227 ******************************************************* PP TIGR03247 222 rfpdaritldpngawsleeaialckdlkdvlayaedpvgaeegysgrevmaefrr 276 rfpdaritldpngawsl+eai+lc+d++ vlayaedp+gae+gysgrevmaefrr lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2480 228 RFPDARITLDPNGAWSLKEAIRLCRDQHRVLAYAEDPCGAENGYSGREVMAEFRR 282 ******************************************************* PP TIGR03247 277 atglptatnmiatdwrelghalrlqavdipladphfwtlqgsvrvaqlceeyglt 331 atgl tatnmiatdwre+gha++lq+vdipladphfwt+qgsvrvaq+c+e+glt lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2480 283 ATGLKTATNMIATDWREMGHAIQLQSVDIPLADPHFWTMQGSVRVAQMCHEWGLT 337 ******************************************************* PP TIGR03247 332 wgshsnnhfdislamfthvaaaapgkvtaidthwiwqdgqrltkepleikegkik 386 wgshsnnhfdislamfthvaaaapg++taidthwiwqdgqrltk+pl+i +g+++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2480 338 WGSHSNNHFDISLAMFTHVAAAAPGEITAIDTHWIWQDGQRLTKAPLQIVDGCVQ 392 ******************************************************* PP TIGR03247 387 vpekpglgveldedavekahelykkkglgarddavamqllipnwkfdekrpclvr 441 vp+kpglgveld+d+v+kahelyk +glgardd+vamq+lip+wkfd+krpclvr lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2480 393 VPQKPGLGVELDMDQVAKAHELYKGMGLGARDDSVAMQFLIPDWKFDNKRPCLVR 447 ******************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (441 nodes) Target sequences: 1 (447 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: 00:00:00.02 # Mc/sec: 7.13 // [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