Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_013840437.1 DESRU_RS01900 citramalate synthase
Query= BRENDA::Q74C76 (528 letters) >NCBI__GCF_000215085.1:WP_013840437.1 Length = 530 Score = 577 bits (1486), Expect = e-169 Identities = 289/520 (55%), Positives = 374/520 (71%), Gaps = 4/520 (0%) Query: 3 LVKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKK 62 L+K+YDT+LRDGTQ E +S EDK++IA +LDE+G HYIEGGWPGSNPKD+ FF +++ Sbjct: 10 LIKIYDTSLRDGTQGEGVSLSAEDKMKIARRLDEMGFHYIEGGWPGSNPKDMEFFARLRQ 69 Query: 63 EKLSQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEEN 122 L A + AFGST R V +D NL L+++ IFGKTWDFHV +AL SLEEN Sbjct: 70 TPLKNALVTAFGSTCRPGVEAARDENLNRLLESGVRAAAIFGKTWDFHVTKALNTSLEEN 129 Query: 123 LELIFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGT 182 L ++ DS+ YLK VF+D EHFFDG+KANPDYA+ L+AA + AD +VLCDTNGGT Sbjct: 130 LRMVRDSVAYLKQQGLTVFFDGEHFFDGFKANPDYALSVLRAAVEGGADAVVLCDTNGGT 189 Query: 183 MPFELVEIIREVRKHIT-APLGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERCGN 241 +P EL ++ V++ + LGIH HND E AVAN++ AV G+ QVQGT+NG GERCGN Sbjct: 190 LPHELQSVVARVKQELPGVELGIHAHNDGEMAVANTIVAVQAGVTQVQGTVNGLGERCGN 249 Query: 242 ANLCSIIPALKLKMKRECIGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAHKGGV 301 ANLCSI+P L LK+ E I + L +LSRFVYE+ANL+P +Q +VG SAFAHKGG+ Sbjct: 250 ANLCSILPNLTLKLGYETIPRENFAFLTELSRFVYEVANLNPVNNQPFVGESAFAHKGGI 309 Query: 302 HVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTLEILE 361 HVSA+ + P TYEH+ PE VGN RVL+S+LSG SN+L K +E + +D P +LE Sbjct: 310 HVSALLKEPGTYEHMPPEWVGNTRRVLMSELSGLSNLLYKYKE--LHLDKSSPEGRRVLE 367 Query: 362 NIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKRHEDQKPLSEATIMV 421 +K ME+RGYQFE AE S E+++++A+ +R+ F + R+I E R ED+ SEA I + Sbjct: 368 QLKNMEHRGYQFEAAEGSLEIMLRKAVNGYREPFQLESMRLILEMR-EDRPIQSEAVIKL 426 Query: 422 KVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVLPAGQGTASSIRV 481 +VG ++ HTAAEGNGPVNALDNALRKALE YP + ++LLDYKVRVL GT + +RV Sbjct: 427 RVGEEVVHTAAEGNGPVNALDNALRKALETVYPEVPGLRLLDYKVRVLEEKAGTEAQVRV 486 Query: 482 LIESGDKESRWGTVGVSENIVDASYQALLDSVEYKLHKSE 521 LIE+G+ + WGTVGVS NI++AS+QAL D + Y L K E Sbjct: 487 LIETGNGKKTWGTVGVSTNIIEASWQALADGMAYGLLKDE 526 Lambda K H 0.317 0.135 0.387 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: 776 Number of extensions: 31 Number of successful extensions: 4 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: 528 Length of database: 530 Length adjustment: 35 Effective length of query: 493 Effective length of database: 495 Effective search space: 244035 Effective search space used: 244035 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 (21.6 bits) S2: 52 (24.6 bits)
Align candidate WP_013840437.1 DESRU_RS01900 (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.419260.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.6e-230 749.2 0.0 1.1e-229 749.0 0.0 1.0 1 NCBI__GCF_000215085.1:WP_013840437.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000215085.1:WP_013840437.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 749.0 0.0 1.1e-229 1.1e-229 2 523 .. 11 528 .. 10 530 .] 0.99 Alignments for each domain: == domain 1 score: 749.0 bits; conditional E-value: 1.1e-229 TIGR00977 2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvvafsst 74 +k+ydt+lrdG+q eGvsls edk++ia++ld++G hyieGGwpg+npkd++ff ++++ +lkna v+af+st NCBI__GCF_000215085.1:WP_013840437.1 11 IKIYDTSLRDGTQGEGVSLSAEDKMKIARRLDEMGFHYIEGGWPGSNPKDMEFFARLRQTPLKNALVTAFGST 83 79*********************************************************************** PP TIGR00977 75 rrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadeviydaehffd 147 rp ++ d++l+ l++++ + +ifGk+wd+hv++al+t+leenl+m+ d+v+ylk+++ v +d ehffd NCBI__GCF_000215085.1:WP_013840437.1 84 CRPGVEAARDENLNRLLESGVRAAAIFGKTWDFHVTKALNTSLEENLRMVRDSVAYLKQQGLTVFFDGEHFFD 156 ************************************************************************* PP TIGR00977 148 GykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrlkdpqlGihahndsetavansllav 220 G+kanp+yal +l++a ++Gad +vl+dtnGGtlphe++ ++ +vk++l +lGihahnd e+avan+++av NCBI__GCF_000215085.1:WP_013840437.1 157 GFKANPDYALSVLRAAVEGGADAVVLCDTNGGTLPHELQSVVARVKQELPGVELGIHAHNDGEMAVANTIVAV 229 ************************************************************************* PP TIGR00977 221 eaGavqvqGtinGlGercGnanlcslipnlqlklgldviekenlkkltevarlvaeivnlaldenmpyvGesa 293 +aG +qvqGt+nGlGercGnanlcs++pnl lklg++ i++en++ lte++r+v e+ nl + +n p+vGesa NCBI__GCF_000215085.1:WP_013840437.1 230 QAGVTQVQGTVNGLGERCGNANLCSILPNLTLKLGYETIPRENFAFLTELSRFVYEVANLNPVNNQPFVGESA 302 ************************************************************************* PP TIGR00977 294 fahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklkelGieidekspkvrkilkkikele 366 fahkGG+hvsa+ ++p tyeh+ pe vGn r++ +sel+G+sn+l k kel ++d++sp+ r++l+++k++e NCBI__GCF_000215085.1:WP_013840437.1 303 FAHKGGIHVSALLKEPGTYEHMPPEWVGNTRRVLMSELSGLSNLLYKYKEL--HLDKSSPEGRRVLEQLKNME 373 *************************************************96..79****************** PP TIGR00977 367 kqGyhfeaaeaslellvrdalGkrkkyfevdgfrvliakrrdeeslseaeatvrvsvegaeeltaaeGnGpvs 439 ++Gy+feaae sle+++r+a+ ++ f+++++r++++ r d sea +++rv +e+ ++taaeGnGpv+ NCBI__GCF_000215085.1:WP_013840437.1 374 HRGYQFEAAEGSLEIMLRKAVNGYREPFQLESMRLILEMREDRPIQSEAVIKLRVGEEV--VHTAAEGNGPVN 444 *************************************9999998888888888888887..59********** PP TIGR00977 440 aldralrkalekfypslkdlkltdykvrilnesaGtsaktrvliessdGkrrwgtvGvseniieasytalles 512 ald+alrkale yp++ l+l+dykvr+l+e+aGt+a++rvlie+ +Gk+ wgtvGvs niieas++al ++ NCBI__GCF_000215085.1:WP_013840437.1 445 ALDNALRKALETVYPEVPGLRLLDYKVRVLEEKAGTEAQVRVLIETGNGKKTWGTVGVSTNIIEASWQALADG 517 ************************************************************************* PP TIGR00977 513 ieyklrkdeee 523 + y+l kde++ NCBI__GCF_000215085.1:WP_013840437.1 518 MAYGLLKDENN 528 ********976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (526 nodes) Target sequences: 1 (530 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 33.34 // [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