Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate WP_106712020.1 CU102_RS15545 citramalate synthase
Query= BRENDA::Q74C76 (528 letters) >NCBI__GCF_003010955.1:WP_106712020.1 Length = 537 Score = 474 bits (1221), Expect = e-138 Identities = 265/532 (49%), Positives = 343/532 (64%), Gaps = 15/532 (2%) Query: 4 VKLYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKKE 63 + L+DTTLRDG Q I F VEDK IA LDE G Y+EGG+PG+NP D AFF + + Sbjct: 6 IYLFDTTLRDGQQTPGIDFSVEDKKVIADMLDEFGFDYVEGGYPGANPTDTAFFAE---K 62 Query: 64 KLSQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEENL 123 + +AK AAFG T+RA V+ D L LI++ D GK+WD+HV AL + EENL Sbjct: 63 RTKRAKFAAFGMTKRAGVSASNDPGLAGLIRSSADTVCFVGKSWDYHVRVALSCTNEENL 122 Query: 124 ELIFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGTM 183 E I S++ E D EHFFDGYKANPDYA+ K A DA A IVLCDTNGG+ Sbjct: 123 ESIDASVKAAIEAGKEAIVDCEHFFDGYKANPDYALACAKTAYDAGARWIVLCDTNGGSQ 182 Query: 184 PFELVEIIREVRKHITAP-LGIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERCGNA 242 P E+ EI+R+V K I LGIH HND+E AVANSL A+ G+ VQGT+NG GERCGNA Sbjct: 183 PAEVAEIVRKVTKLIPGDHLGIHAHNDTEQAVANSLAAIDAGVRHVQGTLNGIGERCGNA 242 Query: 243 NLCSIIPALKLKMK-----RECIGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAFAH 297 NL +IIP L LK I ++L+ L LSR EL N +PN A+VG SAFA Sbjct: 243 NLVTIIPTLMLKPAWSDRFETGISLEKLQGLARLSRSFDELLNRAPNPQGAFVGTSAFAT 302 Query: 298 KGGVHVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPVTL 357 K G+H SA+ + P TYEH+ PE VGN +V+VSD G+SN + + E I + DP Sbjct: 303 KAGIHASALIKEPATYEHVPPETVGNRRKVMVSDQGGKSNFINELERRGIPVAKSDPRLD 362 Query: 358 EILENIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKRHE---DQKPL 414 ++ +KE E GY +EGA+ASFELL +R LGT +FF V FR + E+R + + K + Sbjct: 363 TLIALVKEHEAEGYAYEGADASFELLARRTLGTVPEFFKVDSFRCMVERRFDANGNIKTV 422 Query: 415 SEATIMVKVGGKIEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDYKVRVLPAGQG 474 SEA + V++ G+ + AEG+GPVNALD ALRK + ++ + ++ L D+KVR+L G Sbjct: 423 SEAVVRVEIDGETRMSVAEGHGPVNALDLALRKDMGRYQHEIDDLVLADFKVRIL--NGG 480 Query: 475 TASSIRVLIESGD-KESRWGTVGVSENIVDASYQALLDSVEYKLHKSEEIEG 525 T + RVLIES D +RW TVGVS+NI+DAS+QAL+DSV YKL K+ ++ G Sbjct: 481 TEAITRVLIESTDSSNARWWTVGVSDNIIDASFQALMDSVVYKLMKNRDLAG 532 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: 728 Number of extensions: 28 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_106712020.1 CU102_RS15545 (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.1804797.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-186 605.4 0.0 4.5e-186 605.1 0.0 1.0 1 NCBI__GCF_003010955.1:WP_106712020.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010955.1:WP_106712020.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 605.1 0.0 4.5e-186 4.5e-186 2 521 .. 6 528 .. 5 532 .. 0.96 Alignments for each domain: == domain 1 score: 605.1 bits; conditional E-value: 4.5e-186 TIGR00977 2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvvafsst 74 ++l+dttlrdG q+ G+ +s+edk ia+ ld++G +y+eGG+pganp d+aff + k+ak +af+ t NCBI__GCF_003010955.1:WP_106712020.1 6 IYLFDTTLRDGQQTPGIDFSVEDKKVIADMLDEFGFDYVEGGYPGANPTDTAFFAEK---RTKRAKFAAFGMT 75 89****************************************************865...5689********* PP TIGR00977 75 rrpdkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadeviydaehffd 147 +r + ++d+ l li++ + v Gkswd hv al t eenl+ i +v+ + ++e i d ehffd NCBI__GCF_003010955.1:WP_106712020.1 76 KRAGVSASNDPGLAGLIRSSADTVCFVGKSWDYHVRVALSCTNEENLESIDASVKAAIEAGKEAIVDCEHFFD 148 ************************************************************************* PP TIGR00977 148 GykanpeyalktlkvaekaGadwlvladtnGGtlpheieeitkkvkkrlkdpqlGihahndsetavansllav 220 Gykanp+yal+ k+a +aGa w+vl+dtnGG+ p e+ ei++kv k + +lGihahnd+e avansl+a+ NCBI__GCF_003010955.1:WP_106712020.1 149 GYKANPDYALACAKTAYDAGARWIVLCDTNGGSQPAEVAEIVRKVTKLIPGDHLGIHAHNDTEQAVANSLAAI 221 ************************************************************************* PP TIGR00977 221 eaGavqvqGtinGlGercGnanlcslipnlqlklgl....d.viekenlkkltevarlvaeivnlaldenmpy 288 aG ++vqGt+nG+GercGnanl ++ip l+lk + + i e+l+ l ++r e+ n+a++ + + NCBI__GCF_003010955.1:WP_106712020.1 222 DAGVRHVQGTLNGIGERCGNANLVTIIPTLMLKPAWsdrfEtGISLEKLQGLARLSRSFDELLNRAPNPQGAF 294 *********************************8752222335999*************************** PP TIGR00977 289 vGesafahkGGvhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklkelGieidekspkvrkilkk 361 vG safa k G+h+sa+ ++p tyeh+ pe vGn+rk++vs++ Gksn ++ l+ Gi + +++p++ ++++ NCBI__GCF_003010955.1:WP_106712020.1 295 VGTSAFATKAGIHASALIKEPATYEHVPPETVGNRRKVMVSDQGGKSNFINELERRGIPVAKSDPRLDTLIAL 367 ************************************************************************* PP TIGR00977 362 ikelekqGyhfeaaeaslellvrdalGkrkkyfevdgfrvliakrrdee..slseaeatvrvsvegaeeltaa 432 +ke e++Gy +e+a+as+ell r++lG++ ++f+vd+fr ++++r d++ + +ea vrv ++g + +a NCBI__GCF_003010955.1:WP_106712020.1 368 VKEHEAEGYAYEGADASFELLARRTLGTVPEFFKVDSFRCMVERRFDANgnIKTVSEAVVRVEIDGETRMSVA 440 ***********************************************99633455899*************** PP TIGR00977 433 eGnGpvsaldralrkalekfypslkdlkltdykvrilnesaGtsaktrvliessdG.krrwgtvGvseniiea 504 eG+Gpv+ald alrk + ++ ++ dl l d+kvriln+ Gt+a trvlies+d + rw tvGvs+nii+a NCBI__GCF_003010955.1:WP_106712020.1 441 EGHGPVNALDLALRKDMGRYQHEIDDLVLADFKVRILNG--GTEAITRVLIESTDSsNARWWTVGVSDNIIDA 511 *************************************97..9************97367************** PP TIGR00977 505 sytallesieyklrkde 521 s++al++s++ykl+k+ NCBI__GCF_003010955.1:WP_106712020.1 512 SFQALMDSVVYKLMKNR 528 **************975 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 29.58 // [ok]
This GapMind analysis is from Jul 26 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