Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate 351389 BT1861 2-isopropylmalate synthase (NCBI ptt file)
Query= reanno::Btheta:351389 (498 letters) >FitnessBrowser__Btheta:351389 Length = 498 Score = 979 bits (2530), Expect = 0.0 Identities = 498/498 (100%), Positives = 498/498 (100%) Query: 1 MDNRLFIFDTTLRDGEQVPGCQLNTVEKIQVAKALEALGVDVIEAGFPISSPGDFNSVIE 60 MDNRLFIFDTTLRDGEQVPGCQLNTVEKIQVAKALEALGVDVIEAGFPISSPGDFNSVIE Sbjct: 1 MDNRLFIFDTTLRDGEQVPGCQLNTVEKIQVAKALEALGVDVIEAGFPISSPGDFNSVIE 60 Query: 61 ISKAVTWPTICALTRAVQKDIDVAVDALKFAKHKRIHTGIGTSDSHIKYKFNSNREEIIE 120 ISKAVTWPTICALTRAVQKDIDVAVDALKFAKHKRIHTGIGTSDSHIKYKFNSNREEIIE Sbjct: 61 ISKAVTWPTICALTRAVQKDIDVAVDALKFAKHKRIHTGIGTSDSHIKYKFNSNREEIIE 120 Query: 121 RAVAAVKYARRFVDDVEFYAEDAGRTDNEYLARVVEAVIKAGATVVNIPDTTGYCLPSEY 180 RAVAAVKYARRFVDDVEFYAEDAGRTDNEYLARVVEAVIKAGATVVNIPDTTGYCLPSEY Sbjct: 121 RAVAAVKYARRFVDDVEFYAEDAGRTDNEYLARVVEAVIKAGATVVNIPDTTGYCLPSEY 180 Query: 181 GAKIKYLIDHVDGIDNAILSTHCHNDLGMATANTIAGVLNGARQVEVTINGIGERAGNTA 240 GAKIKYLIDHVDGIDNAILSTHCHNDLGMATANTIAGVLNGARQVEVTINGIGERAGNTA Sbjct: 181 GAKIKYLIDHVDGIDNAILSTHCHNDLGMATANTIAGVLNGARQVEVTINGIGERAGNTA 240 Query: 241 LEEIAMIIKSHHEIDIQTNINTQKIYPTSRMVSSLMNMPVQPNKAIVGRNAFAHSSGIHQ 300 LEEIAMIIKSHHEIDIQTNINTQKIYPTSRMVSSLMNMPVQPNKAIVGRNAFAHSSGIHQ Sbjct: 241 LEEIAMIIKSHHEIDIQTNINTQKIYPTSRMVSSLMNMPVQPNKAIVGRNAFAHSSGIHQ 300 Query: 301 DGVLKNVETYEIIDPHDVGIDDNSIVLTARSGRAALKNRLSLLGVNLDQEKLDKVYEEFL 360 DGVLKNVETYEIIDPHDVGIDDNSIVLTARSGRAALKNRLSLLGVNLDQEKLDKVYEEFL Sbjct: 301 DGVLKNVETYEIIDPHDVGIDDNSIVLTARSGRAALKNRLSLLGVNLDQEKLDKVYEEFL 360 Query: 361 KLADKKKDINDDDVLVLAGADRSQNHRIKLEYLQVTSGVGVRSVASLGLNISGEKFEACA 420 KLADKKKDINDDDVLVLAGADRSQNHRIKLEYLQVTSGVGVRSVASLGLNISGEKFEACA Sbjct: 361 KLADKKKDINDDDVLVLAGADRSQNHRIKLEYLQVTSGVGVRSVASLGLNISGEKFEACA 420 Query: 421 SGNGPVDAAIKALKKIVDRHMTLKEFTIQAISKGSDDVGKVHMQVEYDNQIYYGFGANTD 480 SGNGPVDAAIKALKKIVDRHMTLKEFTIQAISKGSDDVGKVHMQVEYDNQIYYGFGANTD Sbjct: 421 SGNGPVDAAIKALKKIVDRHMTLKEFTIQAISKGSDDVGKVHMQVEYDNQIYYGFGANTD 480 Query: 481 IIAASVEAYIDCINKFKA 498 IIAASVEAYIDCINKFKA Sbjct: 481 IIAASVEAYIDCINKFKA 498 Lambda K H 0.317 0.134 0.377 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: 1020 Number of extensions: 21 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: 498 Length of database: 498 Length adjustment: 34 Effective length of query: 464 Effective length of database: 464 Effective search space: 215296 Effective search space used: 215296 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 351389 BT1861 (2-isopropylmalate synthase (NCBI ptt file))
to HMM TIGR00973 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))
# 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/TIGR00973.hmm # target sequence database: /tmp/gapView.28657.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00973 [M=494] Accession: TIGR00973 Description: leuA_bact: 2-isopropylmalate synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-206 672.6 11.2 1.6e-206 672.5 11.2 1.0 1 lcl|FitnessBrowser__Btheta:351389 BT1861 2-isopropylmalate synthas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:351389 BT1861 2-isopropylmalate synthase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 672.5 11.2 1.6e-206 1.6e-206 1 494 [] 4 494 .. 4 494 .. 0.98 Alignments for each domain: == domain 1 score: 672.5 bits; conditional E-value: 1.6e-206 TIGR00973 1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvglaravek 76 r+ ifdttlrdGeq pg +l++ ek+q+akale lgvd+ieaGfp+ss+gdf++v +i+++v +++++l+rav+k lcl|FitnessBrowser__Btheta:351389 4 RLFIFDTTLRDGEQVPGCQLNTVEKIQVAKALEALGVDVIEAGFPISSPGDFNSVIEISKAVTWPTICALTRAVQK 79 678************************************************************************* PP TIGR00973 77 didaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsaedagrteleflarvv 152 did+a++alk a++kriht i tsd h+++k+ ++++e++er+v+avkya+ fvddvef aedagrt+ e+larvv lcl|FitnessBrowser__Btheta:351389 80 DIDVAVDALKFAKHKRIHTGIGTSDSHIKYKFNSNREEIIERAVAAVKYARRFVDDVEFYAEDAGRTDNEYLARVV 155 **************************************************************************** PP TIGR00973 153 eaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGlavanslaavknGarqvectinG 228 ea+i+aGat++niPdt Gy+lP+eyg+ ik+l ++v +id+ails hch+dlG+a+an++a v nGarqve+tinG lcl|FitnessBrowser__Btheta:351389 156 EAVIKAGATVVNIPDTTGYCLPSEYGAKIKYLIDHVDGIDNAILSTHCHNDLGMATANTIAGVLNGARQVEVTING 231 **************************************************************************** PP TIGR00973 229 iGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgmlvqrnkaivGdnafahesGihqdGvlkn 304 iGeraGn+alee++m++k ++ ++++t+int++iy tsr+vs l +m+vq+nkaivG nafah+sGihqdGvlkn lcl|FitnessBrowser__Btheta:351389 232 IGERAGNTALEEIAMIIKSHHE-IDIQTNINTQKIYPTSRMVSSLMNMPVQPNKAIVGRNAFAHSSGIHQDGVLKN 306 ******************9876.69*************************************************** PP TIGR00973 305 ketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkldeeeldklfekfkeladkkkevfdedlealvleel 380 etyei++p ++G++ + +vl++rsGraalk+rl+ lG++ld+e+ldk++e+f++ladkkk++ d+d+ l+ + lcl|FitnessBrowser__Btheta:351389 307 VETYEIIDPHDVGIDDNSIVLTARSGRAALKNRLSLLGVNLDQEKLDKVYEEFLKLADKKKDINDDDVLVLAGADR 382 *******************************************************************987777766 PP TIGR00973 381 rqeeeeklkleklqvqsgeesvptatvklkvkgeekeaaatGnGpvdavykaiekilelevklleysitakgegkd 456 +++++kle+lqv sg + a + l+++ge+ ea+a+GnGpvda +ka++ki++ ++ l+e++i+a ++g+d lcl|FitnessBrowser__Btheta:351389 383 S--QNHRIKLEYLQVTSGVGVRSVASLGLNISGEKFEACASGNGPVDAAIKALKKIVDRHMTLKEFTIQAISKGSD 456 6..56678******************************************************************** PP TIGR00973 457 algevkvvlelngkkysGrgvatdiveasakayvnaln 494 +g+v++++e++++ y G g++tdi+ as++ay++ +n lcl|FitnessBrowser__Btheta:351389 457 DVGKVHMQVEYDNQIYYGFGANTDIIAASVEAYIDCIN 494 ************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (494 nodes) Target sequences: 1 (498 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 0.00s 00:00:00.01 Elapsed: 00:00:00.02 # Mc/sec: 11.79 // [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