Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_012170314.1 AZC_RS09265 citramalate synthase
Query= BRENDA::Q74C76 (528 letters) >NCBI__GCF_000010525.1:WP_012170314.1 Length = 537 Score = 439 bits (1130), Expect = e-128 Identities = 242/525 (46%), Positives = 331/525 (63%), Gaps = 15/525 (2%) Query: 6 LYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKKEKL 65 L+DTTLRDG Q + F + DK+ + L+ +G+ Y+E G+PG+NP D F +++ Sbjct: 14 LFDTTLRDGAQTNGVDFTLADKLNVIGLLNRLGVDYVEAGYPGANPTDTQLFA---QKRP 70 Query: 66 SQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEENLEL 125 S A++ AFG T+RA + D + L+ AE D K F V AL + EENL Sbjct: 71 SAARVTAFGMTKRAGRSVSNDPGVAALLAAEADAICFVAKASAFQVRVALETTEEENLAS 130 Query: 126 IFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGTMPF 185 I +S+ A E D EHFFDG+K NPD+A+ +AA A A +VLCDTNGGT+P Sbjct: 131 IRESVAAAVAAGREALVDCEHFFDGFKENPDFALACAEAAYQAGARWVVLCDTNGGTLPH 190 Query: 186 ELVEIIREVRKHITAP-LGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERCGNANL 244 E+ I+ V + +GIH HND+E AVANSL AV G Q+QGT+NG GERCGNANL Sbjct: 191 EVEAIVARVTARVPGSHVGIHAHNDTEQAVANSLAAVRAGARQIQGTLNGLGERCGNANL 250 Query: 245 CSIIPALKLKMK-----RECIGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAHKG 299 CS+IP L LK + + L ++ +SR + E+ N SP++H YVG SAFA K Sbjct: 251 CSLIPTLLLKGDYAERFETGVSREALAEIGVVSRTLDEMLNRSPDRHAPYVGESAFATKA 310 Query: 300 GVHVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTLEI 359 G+H SAI + P TYEH+ PE VGN RVLVSD +GRSN+LA+ E + +D DP + Sbjct: 311 GIHASAILKDPATYEHVPPEAVGNQRRVLVSDQAGRSNVLAELERLGVPVDRADPRLARL 370 Query: 360 LENIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKRHE---DQKPLSE 416 L+ +KE E GY +E A+ASF LL +R L + FF+V F V E+R+ + ++E Sbjct: 371 LDEVKEREALGYAYEAADASFALLARRMLHSVPDFFTVERFSVKVERRYNAKGEMTTVAE 430 Query: 417 ATIMVKVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVLPAGQGTA 476 A + V+VG ++ +AAEGNGPVNALD ALRK L K+ P + ++L DY+VR+L GT Sbjct: 431 AIVKVRVGDEVFISAAEGNGPVNALDVALRKDLGKYQPYIAGLRLTDYRVRIL--NGGTE 488 Query: 477 SSIRVLIESGDKE-SRWGTVGVSENIVDASYQALLDSVEYKLHKS 520 + RVL+ES D+ +RW TVGVS NI+DAS++ALLDS+ ++L +S Sbjct: 489 AVTRVLVESTDESGARWTTVGVSPNIIDASFEALLDSITWQLLRS 533 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: 628 Number of extensions: 25 Number of successful extensions: 6 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: 537 Length adjustment: 35 Effective length of query: 493 Effective length of database: 502 Effective search space: 247486 Effective search space used: 247486 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_012170314.1 AZC_RS09265 (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.3351179.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-186 604.9 0.0 6.1e-186 604.6 0.0 1.0 1 NCBI__GCF_000010525.1:WP_012170314.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000010525.1:WP_012170314.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 604.6 0.0 6.1e-186 6.1e-186 2 519 .. 12 532 .. 11 535 .. 0.95 Alignments for each domain: == domain 1 score: 604.6 bits; conditional E-value: 6.1e-186 TIGR00977 2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvvafsst 74 l+l+dttlrdGaq++Gv ++l dk+++ l+ lG++y+e G+pganp d+++f + + a+v+af+ t NCBI__GCF_000010525.1:WP_012170314.1 12 LYLFDTTLRDGAQTNGVDFTLADKLNVIGLLNRLGVDYVEAGYPGANPTDTQLFAQKRP---SAARVTAFGMT 81 89****************************************************98665...5799******* PP TIGR00977 75 rrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadeviydaehffd 147 +r + v++d+ + al+ ae+ + k+ + v al+tt eenl+ i ++v+ ++e + d ehffd NCBI__GCF_000010525.1:WP_012170314.1 82 KRAGRSVSNDPGVAALLAAEADAICFVAKASAFQVRVALETTEEENLASIRESVAAAVAAGREALVDCEHFFD 154 ************************************************************************* PP TIGR00977 148 GykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrlkdpqlGihahndsetavansllav 220 G+k np++al+ ++a +aGa w+vl+dtnGGtlphe+e i+ +v r+ +++Gihahnd+e avansl+av NCBI__GCF_000010525.1:WP_012170314.1 155 GFKENPDFALACAEAAYQAGARWVVLCDTNGGTLPHEVEAIVARVTARVPGSHVGIHAHNDTEQAVANSLAAV 227 ************************************************************************* PP TIGR00977 221 eaGavqvqGtinGlGercGnanlcslipnlqlklgl.....dviekenlkkltevarlvaeivnlaldenmpy 288 +aGa+q+qGt+nGlGercGnanlcslip l lk ++ + +e l+++ v+r + e+ n+++d+++py NCBI__GCF_000010525.1:WP_012170314.1 228 RAGARQIQGTLNGLGERCGNANLCSLIPTLLLKGDYaerfeTGVSREALAEIGVVSRTLDEMLNRSPDRHAPY 300 **********************************994333225899*************************** PP TIGR00977 289 vGesafahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklkelGieidekspkvrkilkk 361 vGesafa k G+h+sa+ ++p tyeh+ pe vGn+r++ vs++aG+snvl l+ lG+ +d+ +p++ ++l++ NCBI__GCF_000010525.1:WP_012170314.1 301 VGESAFATKAGIHASAILKDPATYEHVPPEAVGNQRRVLVSDQAGRSNVLAELERLGVPVDRADPRLARLLDE 373 ************************************************************************* PP TIGR00977 362 ikelekqGyhfeaaeaslellvrdalGkrkkyfevdgfrvliakrrdee....slseaeatvrvsvegaeelt 430 +ke e+ Gy +eaa+as+ ll r++l ++ ++f v+ f v++++r +++ +++ea ++vrv +e NCBI__GCF_000010525.1:WP_012170314.1 374 VKEREALGYAYEAADASFALLARRMLHSVPDFFTVERFSVKVERRYNAKgemtTVAEAIVKVRVGDE--VFIS 444 *******************************************998876544444555555555555..5689 PP TIGR00977 431 aaeGnGpvsaldralrkalekfypslkdlkltdykvrilnesaGtsaktrvliessdGk.rrwgtvGvsenii 502 aaeGnGpv+ald alrk l k+ p ++ l+ltdy+vriln+ Gt+a trvl+es+d rw+tvGvs+nii NCBI__GCF_000010525.1:WP_012170314.1 445 AAEGNGPVNALDVALRKDLGKYQPYIAGLRLTDYRVRILNG--GTEAVTRVLVESTDESgARWTTVGVSPNII 515 ***************************************97..9************965379*********** PP TIGR00977 503 easytallesieyklrk 519 +as+ all+si ++l + NCBI__GCF_000010525.1:WP_012170314.1 516 DASFEALLDSITWQLLR 532 ************99865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (526 nodes) Target sequences: 1 (537 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 0.02s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 13.80 // [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