Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate PfGW456L13_3592 3-isopropylmalate dehydratase large subunit (EC 4.2.1.33)
Query= CharProtDB::CH_024771 (466 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 Length = 473 Score = 507 bits (1306), Expect = e-148 Identities = 248/465 (53%), Positives = 331/465 (71%), Gaps = 6/465 (1%) Query: 3 KTLYEKLFDAHVVYEAENETP-LLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATM 61 +TLY+K D+H V +++ LLYIDR + +E TSPQAF G+R GR +PG T A + Sbjct: 5 RTLYQKHIDSHTVCALDDQGHVLLYIDRQVANEYTSPQAFSGMREAGRKAWRPGATLAVV 64 Query: 62 DH---NVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVT 118 DH V T+T + G ++ E +NC++FG+EL+D+ QGI HV+ PEQG Sbjct: 65 DHVNPTVPTRTAAMPDAGGARQVSYFE--ENCRDFGIELFDVLDKRQGIEHVVAPEQGFI 122 Query: 119 LPGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGI 178 LPGM + GDSHT T+GA GA FGIGTSE+EH+LA+QTL R KTM++ V G G+ Sbjct: 123 LPGMVVAAGDSHTTTYGALGAFGFGIGTSEIEHLLASQTLVYKRLKTMRVTVNGVLGTGV 182 Query: 179 TAKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDET 238 T+KDI++A+I K G++G TG+ +EF G AI DLS+E RMT+CNMA+E GA+ +APD+ Sbjct: 183 TSKDIIMALIEKIGASGATGYAIEFAGPAISDLSVEARMTICNMAVEAGARGAFMAPDDK 242 Query: 239 TFNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVI 298 F Y++ + AP+G+ ++ AVA W+ L +DEGA FD VTL + P VTWGT+P Q Sbjct: 243 VFAYLQHKPRAPQGQLWEQAVAKWRGLHSDEGAVFDREVTLDVAALEPMVTWGTSPDQAA 302 Query: 299 SVNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAA 358 SV ++PDPA+ D + R ++AL YMGL PG+PL++V I FIGSCTN+RIEDLR Sbjct: 303 SVGGHVPDPAAQPDLILRQGMQRALNYMGLTPGMPLSDVVISHAFIGSCTNARIEDLRDV 362 Query: 359 AEIAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRL 418 A + +G++VA V+A++VPGS V+ QAE EGL +IF++AGFEWR GCSMCLAMN+D L Sbjct: 363 ARVVRGKRVASHVRAMIVPGSTLVRHQAEDEGLAQIFLDAGFEWRQSGCSMCLAMNDDVL 422 Query: 419 NPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463 PG+RCAS++NRNFEGRQG G RTHL+SPAM AAAA+TGH D+R Sbjct: 423 APGDRCASSTNRNFEGRQGAGARTHLMSPAMVAAAAITGHLTDVR 467 Lambda K H 0.317 0.134 0.396 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: 694 Number of extensions: 29 Number of successful extensions: 3 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: 466 Length of database: 473 Length adjustment: 33 Effective length of query: 433 Effective length of database: 440 Effective search space: 190520 Effective search space used: 190520 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: 51 (24.3 bits)
Align candidate PfGW456L13_3592 (3-isopropylmalate dehydratase large subunit (EC 4.2.1.33))
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))
# 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.aa/TIGR00170.hmm # target sequence database: /tmp/gapView.3035580.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00170 [M=466] Accession: TIGR00170 Description: leuC: 3-isopropylmalate dehydratase, large subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.4e-199 647.0 0.0 8.5e-199 646.8 0.0 1.0 1 FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 Domain annotation for each sequence (and alignments): >> FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 646.8 0.0 8.5e-199 8.5e-199 2 466 .] 4 469 .. 3 469 .. 0.98 Alignments for each domain: == domain 1 score: 646.8 bits; conditional E-value: 8.5e-199 TIGR00170 2 aktlyeklfdahvvke.aenetdllyidrhlvhevtspqafeglraagrkvrrvdktla 59 ++tly+k d+h v ++++ llyidr + e tspqaf g+r+agrk r++ tla FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 4 PRTLYQKHIDSHTVCAlDDQGHVLLYIDRQVANEYTSPQAFSGMREAGRKAWRPGATLA 62 89**********987626677889*********************************** PP TIGR00170 60 tldhniste.srdveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegl 117 +dh +t+ +r + + +qv +e+n+++fg++lfd+ +++qgi hvv pe+g+ FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 63 VVDHVNPTVpTRTAAMPDAGGARQVSYFEENCRDFGIELFDVLDKRQGIEHVVAPEQGF 121 ****999973566677788899************************************* PP TIGR00170 118 tlpgktivcgdshtathgafgalafgigtsevehvlatqtlkqaraktlkievegklak 176 lpg+ + gdsht+t+ga+ga+ fgigtse+eh+la+qtl+ +r kt++++v+g l + FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 122 ILPGMVVAAGDSHTTTYGALGAFGFGIGTSEIEHLLASQTLVYKRLKTMRVTVNGVLGT 180 *********************************************************** PP TIGR00170 177 gitakdiilaiigkigvaggtgyvvefageairdlsmeermtvcnmaieagakagliap 235 g+t+kdii+a+i kig++g tgy +efag ai dls+e+rmt+cnma+eaga+ ++ap FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 181 GVTSKDIIMALIEKIGASGATGYAIEFAGPAISDLSVEARMTICNMAVEAGARGAFMAP 239 *********************************************************** PP TIGR00170 236 dettfeyvkdrkyapkgkefekavaywktlktdegakfdkvvtleakdispqvtwgtnp 294 d+ f+y+++++ ap+g+ +e+ava+w+ l++dega+fd++vtl+ + p+vtwgt+p FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 240 DDKVFAYLQHKPRAPQGQLWEQAVAKWRGLHSDEGAVFDREVTLDVAALEPMVTWGTSP 298 *********************************************************** PP TIGR00170 295 gqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigsctnsrie 353 +q+ sv ++vpdp+ d + ++++++al+y+gl+pg++l d+ + + figsctn+rie FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 299 DQAASVGGHVPDPAAQPDLILRQGMQRALNYMGLTPGMPLSDVVISHAFIGSCTNARIE 357 *********************************************************** PP TIGR00170 354 dlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslcl 412 dlr a vv+gk+va+ v+ a++vpgs lv++qae egl +ifl+agfewr++gcs+cl FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 358 DLRDVARVVRGKRVASHVR-AMIVPGSTLVRHQAEDEGLAQIFLDAGFEWRQSGCSMCL 415 *******************.*************************************** PP TIGR00170 413 gmnndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdirel 466 +mn+dvl +++rcas++nrnfegrqg+garthl+spam aaaa++g++ d+r + FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3592 416 AMNDDVLAPGDRCASSTNRNFEGRQGAGARTHLMSPAMVAAAAITGHLTDVRTF 469 ****************************************************76 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (473 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: 00:00:00.01 # Mc/sec: 13.97 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
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