Align 3-isopropylmalate dehydratase large subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate AZOBR_RS03545 AZOBR_RS03545 isopropylmalate isomerase
Query= SwissProt::P15717 (466 letters) >FitnessBrowser__azobra:AZOBR_RS03545 Length = 467 Score = 642 bits (1657), Expect = 0.0 Identities = 318/463 (68%), Positives = 372/463 (80%) Query: 3 KTLYEKLFDAHVVFEAPNETPLLYIDRHLVHEVTSPQAFDGLRAHHRPVRQPGKTFATMD 62 +TL++K++D+HVV + T +LYIDRHLVHEVTSPQAF+GLR RPVR+P T A D Sbjct: 5 RTLFDKIWDSHVVHRQDDGTCILYIDRHLVHEVTSPQAFEGLRLAGRPVRRPEATLAVPD 64 Query: 63 HNVSTQTKDINASGEMARIQMQELIKNCNEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122 HNV T + E +RIQ++ L KN +FGV + ++ QGIVH++GPEQG TLPG Sbjct: 65 HNVPTTDRSKGIVEEESRIQVETLDKNARDFGVRYFPMDDVRQGIVHIVGPEQGFTLPGA 124 Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVTGNAAPGITAKD 182 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTL Q AK M + V G G+TAKD Sbjct: 125 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLLQKPAKNMLVRVDGELPAGVTAKD 184 Query: 183 IVLAIIGKTGSAGGTGHVVEFCGDAIRALSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242 IVLAIIG+ G+AGGTGHV+EF GDAIR LSMEGRMT+CNMAIE GA+AGL+APDE TF Y Sbjct: 185 IVLAIIGRIGTAGGTGHVIEFAGDAIRGLSMEGRMTVCNMAIEGGARAGLIAPDEKTFEY 244 Query: 243 VKGRLHAPKGRDFDEAVEYWKTLKTDDGATFDTVVALRAEEIAPQVTWGTNPGQVISVTD 302 VKGR APK +++AVEYWKTL +D+GA +DT V L A +I PQVTWGT+P V+ +T Sbjct: 245 VKGRALAPKAGAWEQAVEYWKTLPSDEGAVYDTTVVLNAADIVPQVTWGTSPEDVLPITA 304 Query: 303 IIPDPASFSDPVERASAEKALAYMGLQPGVPLTDVAIDKVFIGSCTNSRIEDLRAAAEVA 362 +P+PA +D +RA+ E++LAYMGL+PG LTDV +D VFIGSCTN RIEDLRAAA +A Sbjct: 305 TVPNPADVADAGKRAAVERSLAYMGLEPGQKLTDVKVDTVFIGSCTNGRIEDLRAAAVIA 364 Query: 363 KGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGE 422 +GRKVA GV+ALVVPGSG VK QAE EGLDKIF EAGFEWR PGCSMCLAMN DRL+PGE Sbjct: 365 QGRKVAEGVRALVVPGSGLVKDQAEEEGLDKIFTEAGFEWREPGCSMCLAMNADRLSPGE 424 Query: 423 RCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRSI 465 R ASTSNRNFEGRQGRGGRTHL+SPAMAAAAAVTGH D+RS+ Sbjct: 425 RSASTSNRNFEGRQGRGGRTHLLSPAMAAAAAVTGHLTDVRSL 467 Lambda K H 0.318 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: 817 Number of extensions: 30 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: 466 Length of database: 467 Length adjustment: 33 Effective length of query: 433 Effective length of database: 434 Effective search space: 187922 Effective search space used: 187922 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 AZOBR_RS03545 AZOBR_RS03545 (isopropylmalate isomerase)
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.29292.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-251 820.0 0.1 3.1e-251 819.8 0.1 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS03545 AZOBR_RS03545 isopropylmalate is Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS03545 AZOBR_RS03545 isopropylmalate isomerase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 819.8 0.1 3.1e-251 3.1e-251 2 465 .. 4 466 .. 3 467 .] 1.00 Alignments for each domain: == domain 1 score: 819.8 bits; conditional E-value: 3.1e-251 TIGR00170 2 aktlyeklfdahvvkeaenetdllyidrhlvhevtspqafeglraagrkvrrvdktlatldhnistesr 70 ++tl++k++d+hvv++++++t +lyidrhlvhevtspqafeglr agr+vrr++ tla dhn++t+ r lcl|FitnessBrowser__azobra:AZOBR_RS03545 4 PRTLFDKIWDSHVVHRQDDGTCILYIDRHLVHEVTSPQAFEGLRLAGRPVRRPEATLAVPDHNVPTTDR 72 89******************************************************************* PP TIGR00170 71 dveikeekaklqvkeleknvkefgvklfdlssaeqgivhvvgpeegltlpgktivcgdshtathgafga 139 i+ee++++qv++l+kn+++fgv++f +++++qgivh+vgpe+g+tlpg tivcgdshtathgafga lcl|FitnessBrowser__azobra:AZOBR_RS03545 73 SKGIVEEESRIQVETLDKNARDFGVRYFPMDDVRQGIVHIVGPEQGFTLPGATIVCGDSHTATHGAFGA 141 ********************************************************************* PP TIGR00170 140 lafgigtsevehvlatqtlkqaraktlkievegklakgitakdiilaiigkigvaggtgyvvefageai 208 lafgigtsevehvlatqtl q+ ak++ ++v+g+l g+takdi+laiig+ig+aggtg+v+efag+ai lcl|FitnessBrowser__azobra:AZOBR_RS03545 142 LAFGIGTSEVEHVLATQTLLQKPAKNMLVRVDGELPAGVTAKDIVLAIIGRIGTAGGTGHVIEFAGDAI 210 ********************************************************************* PP TIGR00170 209 rdlsmeermtvcnmaieagakagliapdettfeyvkdrkyapkgkefekavaywktlktdegakfdkvv 277 r lsme+rmtvcnmaie ga+agliapde tfeyvk+r +apk +e+av+ywktl +dega++d++v lcl|FitnessBrowser__azobra:AZOBR_RS03545 211 RGLSMEGRMTVCNMAIEGGARAGLIAPDEKTFEYVKGRALAPKAGAWEQAVEYWKTLPSDEGAVYDTTV 279 ********************************************************************* PP TIGR00170 278 tleakdispqvtwgtnpgqvlsvneevpdpksladpvekasaekalaylglepgtklkdikvdkvfigs 346 +l+a di+pqvtwgt+p++vl+++ +vp+p+++ad ++a +e++lay+glepg+kl+d+kvd vfigs lcl|FitnessBrowser__azobra:AZOBR_RS03545 280 VLNAADIVPQVTWGTSPEDVLPITATVPNPADVADAGKRAAVERSLAYMGLEPGQKLTDVKVDTVFIGS 348 ********************************************************************* PP TIGR00170 347 ctnsriedlraaaevvkgkkvadnvklalvvpgsglvkkqaekegldkifleagfewreagcslclgmn 415 ctn+riedlraaa +++g+kva++v+ alvvpgsglvk qae+egldkif eagfewre+gcs+cl+mn lcl|FitnessBrowser__azobra:AZOBR_RS03545 349 CTNGRIEDLRAAAVIAQGRKVAEGVR-ALVVPGSGLVKDQAEEEGLDKIFTEAGFEWREPGCSMCLAMN 416 **************************.****************************************** PP TIGR00170 416 ndvldeyercastsnrnfegrqgkgarthlvspamaaaaavagkfvdire 465 d+l+++er astsnrnfegrqg+g+rthl+spamaaaaav+g++ d+r lcl|FitnessBrowser__azobra:AZOBR_RS03545 417 ADRLSPGERSASTSNRNFEGRQGRGGRTHLLSPAMAAAAAVTGHLTDVRS 466 ************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (466 nodes) Target sequences: 1 (467 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: 00:00:00.02 # Mc/sec: 9.22 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 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