Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate WP_020565658.1 A3OW_RS0122190 2-isopropylmalate synthase
Query= BRENDA::Q9JZG1 (517 letters) >NCBI__GCF_000372865.1:WP_020565658.1 Length = 514 Score = 630 bits (1626), Expect = 0.0 Identities = 316/498 (63%), Positives = 393/498 (78%) Query: 5 NRVIIFDTTLRDGEQSPGAAMTKEEKIRVARQLEKLGVDIIEAGFAAASPGDFEAVNAIA 64 +++IIFDTT+RDGEQSPGA+MT++EKIR+ + LE+L VD+IEAGF AASPGDFEAV A+A Sbjct: 3 DKLIIFDTTMRDGEQSPGASMTRDEKIRIGKALERLKVDVIEAGFPAASPGDFEAVQAVA 62 Query: 65 KTITKSTVCSLSRAIERDIRQAGEAVAPAPKKRIHTFIATSPIHMEYKLKMKPKQVIEAA 124 I STVC L+RA+++DI AG A+ A + RIHTFIATSPIHM+ KL M+P+QVIE A Sbjct: 63 NVIKDSTVCGLARALDKDIDSAGLALKGAARSRIHTFIATSPIHMQMKLHMQPEQVIEYA 122 Query: 125 VKAVKIAREYTDDVEFSCEDALRSEIDFLAEICGAVIEAGATTINIPDTVGYSIPYKTEE 184 V+AVK AR+YTDDVEFS EDA RSE DFL I AVI+AGATT+NIPDTVGYSIP + Sbjct: 123 VRAVKRARQYTDDVEFSPEDAGRSEEDFLCRILEAVIDAGATTLNIPDTVGYSIPQQFGA 182 Query: 185 FFRELIAKTPNGGKVVWSAHCHNDLGLAVANSLAALKGGARQVECTVNGLGERAGNASVE 244 LI + PN K V+S HCHNDLGLAVANSL+A+ GARQ+ECT+NGLGERAGNAS+E Sbjct: 183 TIANLIKRIPNSDKAVFSVHCHNDLGLAVANSLSAVMNGARQIECTINGLGERAGNASLE 242 Query: 245 EIVMALKVRHDLFGLETGIDTTQIVPSSKLVSTITGYPVQPNKAIVGANAFSHESGIHQD 304 E+VMA++ R D+F +TGIDT +I+ SKLVS+ITG+PVQPNKAIVGANAF+HE+GIHQD Sbjct: 243 EVVMAVRTRQDVFTCDTGIDTREILTCSKLVSSITGFPVQPNKAIVGANAFAHEAGIHQD 302 Query: 305 GVLKHRETYEIMSAESVGWATNRLSLGKLSGRNAFKTKLADLGIELESEEALNAAFARFK 364 GVLK RETYEIM AE VGW+ NR+ LGK SGRNAFK+++ +LGIE SEE LN F RFK Sbjct: 303 GVLKSRETYEIMRAEDVGWSANRMVLGKHSGRNAFKSRMTELGIEFTSEEELNDVFLRFK 362 Query: 365 ELADKKREIFDEDLHALVSDEMGSMNAESYKFISQKISTETGEEPRADIVFSIKGEEKRA 424 +LADKK +IFDEDL AL+S+ E K IS K+ +ETGE P A + I +E Sbjct: 363 QLADKKHDIFDEDLQALISEASFESEDEYVKLISLKVCSETGEVPNAKVTLRIDNKEVTG 422 Query: 425 SATGSGPVDAIFKAIESVAQSGAALQIYSVNAVTQGTESQGETSVRLARGNRVVNGQGAD 484 ++ G G VDA KAIE + S A+L++YSVN +T GT+SQGE +VRL + R+VNG GAD Sbjct: 423 NSHGGGAVDASLKAIEQLVMSNASLELYSVNNITNGTDSQGEVTVRLEKEGRIVNGLGAD 482 Query: 485 TDVLVATAKAYLSALSKL 502 TD+++A+AKAY++A++KL Sbjct: 483 TDIVIASAKAYINAVNKL 500 Lambda K H 0.313 0.129 0.352 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: 679 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: 517 Length of database: 514 Length adjustment: 35 Effective length of query: 482 Effective length of database: 479 Effective search space: 230878 Effective search space used: 230878 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 52 (24.6 bits)
Align candidate WP_020565658.1 A3OW_RS0122190 (2-isopropylmalate synthase)
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.7897.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-222 724.8 6.3 2.5e-222 724.6 6.3 1.0 1 lcl|NCBI__GCF_000372865.1:WP_020565658.1 A3OW_RS0122190 2-isopropylmalate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000372865.1:WP_020565658.1 A3OW_RS0122190 2-isopropylmalate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 724.6 6.3 2.5e-222 2.5e-222 1 494 [] 4 498 .. 4 498 .. 0.99 Alignments for each domain: == domain 1 score: 724.6 bits; conditional E-value: 2.5e-222 TIGR00973 1 rvlifdttlrdGeqapgasltveeklqiakalerlgvdiieaGfpvsskgdfeavqkiarevknarvvg 69 +++ifdtt+rdGeq+pgas+t +ek++i kalerl vd+ieaGfp++s+gdfeavq +a+ +k+++v+g lcl|NCBI__GCF_000372865.1:WP_020565658.1 4 KLIIFDTTMRDGEQSPGASMTRDEKIRIGKALERLKVDVIEAGFPAASPGDFEAVQAVANVIKDSTVCG 72 689****************************************************************** PP TIGR00973 70 laravekdidaaaealkpaekkrihtfiatsdihleaklkktkdevlerivkavkyaknfvddvefsae 138 lara++kdid a alk a++ rihtfiats+ih+++kl+++ ++v+e +v+avk+a++++ddvefs+e lcl|NCBI__GCF_000372865.1:WP_020565658.1 73 LARALDKDIDSAGLALKGAARSRIHTFIATSPIHMQMKLHMQPEQVIEYAVRAVKRARQYTDDVEFSPE 141 ********************************************************************* PP TIGR00973 139 dagrteleflarvveaaieaGattiniPdtvGyalPaeygelikelkenvPnidkailsvhchddlGla 207 dagr+e +fl+r++ea+i+aGatt+niPdtvGy +P+++g+ i++l +++Pn dka++svhch+dlGla lcl|NCBI__GCF_000372865.1:WP_020565658.1 142 DAGRSEEDFLCRILEAVIDAGATTLNIPDTVGYSIPQQFGATIANLIKRIPNSDKAVFSVHCHNDLGLA 210 ********************************************************************* PP TIGR00973 208 vanslaavknGarqvectinGiGeraGnaaleevvmalkvrkdflnvetgintkeiyrtsrlvskltgm 276 vansl+av nGarq+ectinG+GeraGna+leevvma+++r+d++ +tgi+t+ei s+lvs +tg lcl|NCBI__GCF_000372865.1:WP_020565658.1 211 VANSLSAVMNGARQIECTINGLGERAGNASLEEVVMAVRTRQDVFTCDTGIDTREILTCSKLVSSITGF 279 ********************************************************************* PP TIGR00973 277 lvqrnkaivGdnafahesGihqdGvlknketyeilspesiGlkkeklvlgkrsGraalkkrleelGfkl 345 +vq+nkaivG+nafahe+GihqdGvlk +etyei+++e++G +++++vlgk+sGr+a+k+r++elG+++ lcl|NCBI__GCF_000372865.1:WP_020565658.1 280 PVQPNKAIVGANAFAHEAGIHQDGVLKSRETYEIMRAEDVGWSANRMVLGKHSGRNAFKSRMTELGIEF 348 ********************************************************************9 PP TIGR00973 346 d.eeeldklfekfkeladkkkevfdedlealvleelrqeeeeklkleklqvqsgeesvptatvklkvkg 413 + eeel+ +f +fk+ladkk+++fdedl+al++e + e+e +kl +l+v s + +vp a v+l++++ lcl|NCBI__GCF_000372865.1:WP_020565658.1 349 TsEEELNDVFLRFKQLADKKHDIFDEDLQALISEASFESEDEYVKLISLKVCSETGEVPNAKVTLRIDN 417 62679*******************************9999999************************** PP TIGR00973 414 eekeaaatGnGpvdavykaiekilelevklleysitakgegkdalgevkvvlelngkkysGrgvatdiv 482 +e + + G G+vda +kaie+++ + l+ ys++ ++g+d++gev+v+le +g+ ++G g++tdiv lcl|NCBI__GCF_000372865.1:WP_020565658.1 418 KEVTGNSHGGGAVDASLKAIEQLVMSNASLELYSVNNITNGTDSQGEVTVRLEKEGRIVNGLGADTDIV 486 ********************************************************************* PP TIGR00973 483 easakayvnaln 494 asakay+na+n lcl|NCBI__GCF_000372865.1:WP_020565658.1 487 IASAKAYINAVN 498 ***********9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (494 nodes) Target sequences: 1 (514 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: 12.75 // [ok]
This GapMind analysis is from Apr 10 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