Align (R)-citramalate synthase; EC 2.3.3.21 (uncharacterized)
to candidate WP_011319948.1 AVA_RS16285 citramalate synthase
Query= curated2:P74269 (547 letters) >NCBI__GCF_000204075.1:WP_011319948.1 Length = 577 Score = 753 bits (1945), Expect = 0.0 Identities = 384/560 (68%), Positives = 431/560 (76%), Gaps = 36/560 (6%) Query: 8 LWLYDTTLRDGAQREGISLSLTDKLTIARRLDQLGIPFIEGGWPGANPKDVQFFWQLQEE 67 +WLYDTTLRDG QREG+S+S DKL IA RLDQLGIPFIEGGWPGANPKDVQFFWQLQE+ Sbjct: 9 IWLYDTTLRDGTQREGLSISTEDKLRIAHRLDQLGIPFIEGGWPGANPKDVQFFWQLQED 68 Query: 68 PLEQAEIVAFCSTRRPHKAVETDKMLQAILSAGTRWVTIFGKSWDLHVLEGLQTSLAENL 127 PL+ ++IVAFCSTRRPH + MLQ IL+AG+ WVTIFGKSWDLHV GL+T+L ENL Sbjct: 69 PLKLSQIVAFCSTRRPHTHAADEPMLQDILAAGSSWVTIFGKSWDLHVTTGLKTTLEENL 128 Query: 128 AMISDTIAYLRSQGRRVIYDAEHWFDGYRANPDYALATLATAQQAGAEWLVMCDTNGGTL 187 AMI DTI + RSQGRRVIYDAEHWFDGY+ N DYAL TL A AGAEWLV+CDTNGGTL Sbjct: 129 AMIRDTIEFFRSQGRRVIYDAEHWFDGYKHNRDYALQTLKAAMAAGAEWLVLCDTNGGTL 188 Query: 188 PGQISEI---TTKVRRSLG-LDGQSDRQ-----------------------------PQL 214 P ++S+I KV R G ++ + D+ PQ+ Sbjct: 189 PHEVSQIVQDVVKVTRDWGRINSKLDQSGQVVSEEVEKSTNSLPNTQYPIPNLPFPIPQI 248 Query: 215 GIHAHNDSGTAVANSLLAVEAGATMVQGTINGYGERCGNANLCTLIPNLQLKLDYDCIEP 274 GIH HNDS AVAN+L AV AGATMVQGTINGYGERCGNANLC+LIPNLQLKL Y CI Sbjct: 249 GIHTHNDSDMAVANALAAVMAGATMVQGTINGYGERCGNANLCSLIPNLQLKLGYSCITE 308 Query: 275 EKLAHLTSTSRLISEIVNLAPDDHAPFVGRSAFAHKGGIHVSAVQRNPFTYEHIAPNLVG 334 +L L SR +SE+VNLAPD+HAPFVGRSAFAHKGGIHVSAV+RNP TYEHI P VG Sbjct: 309 HQLGQLAEASRFVSEVVNLAPDEHAPFVGRSAFAHKGGIHVSAVERNPLTYEHIQPEQVG 368 Query: 335 NERRIVVSEQAGLSNVLSKAELFGIALDRQNPACRTILATLKDLEQQGYQFEAAEASFEL 394 N RRIV+SEQ+G+SNVL+KA FGI LD+Q P + IL LK+LE +GYQFEAAEASF L Sbjct: 369 NRRRIVISEQSGISNVLAKARTFGIELDKQTPEAKQILQRLKELESEGYQFEAAEASFAL 428 Query: 395 LMRQAMGDRQPLFLVQGFQVHCDLLTPAENPAYRNALATVKVTVNGQNILEVAEGNGPVS 454 LM +A+G RQ F V+GFQVHCDL+ E NALATVKV VNG+NILE AEGNGPV+ Sbjct: 429 LMYEALGGRQQFFEVKGFQVHCDLV---EGKEMTNALATVKVAVNGKNILEAAEGNGPVA 485 Query: 455 ALDQALRKALTRFYPQIADFHLTDYKVRILDGGAGTSAKTRVLVESSNGDRRWTTVGVSG 514 ALD ALRKAL FYPQ+A F LTDYKVRILDG GTSAKTR LVES NG +RWTTVGVS Sbjct: 486 ALDAALRKALVNFYPQLATFELTDYKVRILDGHTGTSAKTRALVESGNGYQRWTTVGVSP 545 Query: 515 NILEASYQAVVEGIEYGLRL 534 NIL ASYQAVVEG+EYGL L Sbjct: 546 NILAASYQAVVEGLEYGLLL 565 Lambda K H 0.318 0.134 0.393 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: 909 Number of extensions: 28 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 547 Length of database: 577 Length adjustment: 36 Effective length of query: 511 Effective length of database: 541 Effective search space: 276451 Effective search space used: 276451 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: 53 (25.0 bits)
Align candidate WP_011319948.1 AVA_RS16285 (citramalate synthase)
to HMM TIGR00977 (cimA: citramalate synthase (EC 2.3.1.182))
# 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/TIGR00977.hmm # target sequence database: /tmp/gapView.2700161.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00977 [M=526] Accession: TIGR00977 Description: citramal_synth: citramalate 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-262 858.0 0.1 5.3e-262 855.6 0.1 1.8 1 NCBI__GCF_000204075.1:WP_011319948.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000204075.1:WP_011319948.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 855.6 0.1 5.3e-262 5.3e-262 2 520 .. 9 566 .. 8 572 .. 0.99 Alignments for each domain: == domain 1 score: 855.6 bits; conditional E-value: 5.3e-262 TIGR00977 2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvvafsst 74 ++lydttlrdG+q+eG+s+s edk+ria++ld+lGi++ieGGwpganpkdv+ff++++e +lk ++vaf+st NCBI__GCF_000204075.1:WP_011319948.1 9 IWLYDTTLRDGTQREGLSISTEDKLRIAHRLDQLGIPFIEGGWPGANPKDVQFFWQLQEDPLKLSQIVAFCST 81 8************************************************************************ PP TIGR00977 75 rrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadeviydaehffd 147 rrp+ + ++++lq ++ a++ +vtifGkswdlhv+ +lkttleenl+mi dt+e++++++++viydaeh+fd NCBI__GCF_000204075.1:WP_011319948.1 82 RRPHTHAADEPMLQDILAAGSSWVTIFGKSWDLHVTTGLKTTLEENLAMIRDTIEFFRSQGRRVIYDAEHWFD 154 ************************************************************************* PP TIGR00977 148 GykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrl........................ 196 Gyk n++yal+tlk+a aGa+wlvl+dtnGGtlphe+++i+++v k NCBI__GCF_000204075.1:WP_011319948.1 155 GYKHNRDYALQTLKAAMAAGAEWLVLCDTNGGTLPHEVSQIVQDVVKVTrdwgrinskldqsgqvvseeveks 227 ********************************************99888899********************* PP TIGR00977 197 ................kdpqlGihahndsetavansllaveaGavqvqGtinGlGercGnanlcslipnlqlk 253 pq+Gih+hnds++avan+l+av aGa++vqGtinG+GercGnanlcslipnlqlk NCBI__GCF_000204075.1:WP_011319948.1 228 tnslpntqypipnlpfPIPQIGIHTHNDSDMAVANALAAVMAGATMVQGTINGYGERCGNANLCSLIPNLQLK 300 *************99999******************************************************* PP TIGR00977 254 lgldviekenlkkltevarlvaeivnlaldenmpyvGesafahkGGvhvsavkrnpktyehidpelvGnkrki 326 lg+ +i + +l +l e +r+v+e+vnla+de++p+vG+safahkGG+hvsav+rnp tyehi+pe vGn+r+i NCBI__GCF_000204075.1:WP_011319948.1 301 LGYSCITEHQLGQLAEASRFVSEVVNLAPDEHAPFVGRSAFAHKGGIHVSAVERNPLTYEHIQPEQVGNRRRI 373 ************************************************************************* PP TIGR00977 327 vvselaGksnvleklkelGieidekspkvrkilkkikelekqGyhfeaaeaslellvrdalGkrkkyfevdgf 399 v+se++G snvl k++ +Gie+d+++p+ ++il+++kele +Gy+feaaeas+ ll+ +alG r+++fev+gf NCBI__GCF_000204075.1:WP_011319948.1 374 VISEQSGISNVLAKARTFGIELDKQTPEAKQILQRLKELESEGYQFEAAEASFALLMYEALGGRQQFFEVKGF 446 ************************************************************************* PP TIGR00977 400 rvliakrrdeeslseaeatvrvsvegaeeltaaeGnGpvsaldralrkalekfypslkdlkltdykvrilnes 472 +v++++ + +++a+atv+v+v+g+++l+aaeGnGpv ald alrkal +fyp+l+ ++ltdykvril+++ NCBI__GCF_000204075.1:WP_011319948.1 447 QVHCDLVEGK-EMTNALATVKVAVNGKNILEAAEGNGPVAALDAALRKALVNFYPQLATFELTDYKVRILDGH 518 ******9988.689*********************************************************** PP TIGR00977 473 aGtsaktrvliessdGkrrwgtvGvseniieasytallesieyklrkd 520 +Gtsaktr l+es +G +rw+tvGvs+ni+ asy+a++e++ey+l + NCBI__GCF_000204075.1:WP_011319948.1 519 TGTSAKTRALVESGNGYQRWTTVGVSPNILAASYQAVVEGLEYGLLLH 566 ********************************************9765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (526 nodes) Target sequences: 1 (577 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 0.00s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 13.22 // [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