Align (R)-citramalate synthase (EC 2.3.3.21) (characterized)
to candidate GFF1624 PGA1_c16460 2-isopropylmalate synthase/homocitrate synthase-like protein
Query= BRENDA::Q74C76 (528 letters) >FitnessBrowser__Phaeo:GFF1624 Length = 543 Score = 424 bits (1090), Expect = e-123 Identities = 243/542 (44%), Positives = 336/542 (61%), Gaps = 31/542 (5%) Query: 6 LYDTTLRDGTQAEDISFLVEDKIRIAHKLDEIGIHYIEGGWPGSNPKDVAFFKDIKKEKL 65 LYDTTLRDG Q + + F +K++IA LD +G+ YIEGGWPG+NP D FF + Sbjct: 8 LYDTTLRDGQQTQGVQFSTTEKVQIATALDGLGVDYIEGGWPGANPTDSGFFDAAPR--- 64 Query: 66 SQAKIAAFGSTRRAKVTPDKDHNLKTLIQAEPDVCTIFGKTWDFHVHEALRISLEENLEL 125 ++A + AFG T+RA + + D L ++ A + GK+ D+HV AL I+LEENL+ Sbjct: 65 TRATMTAFGMTKRAGRSAENDDVLAAVLNAGTAAVCLVGKSHDYHVTHALGITLEENLDN 124 Query: 126 IFDSLEYLKANVPEVFYDAEHFFDGYKANPDYAIKTLKAAQDAKADCIVLCDTNGGTMPF 185 I S+ +L A E +DAEHFFDGYK NPDYA+ +AA +A A +VLCDTNGGT+P Sbjct: 125 IRASIAHLVAQGREALFDAEHFFDGYKDNPDYALAACRAALEAGARWVVLCDTNGGTLPG 184 Query: 186 ELVEIIREVRKHITAPL-----GIHTHNDSECAVANSLHAVSEGIVQVQGTINGFGERCG 240 ++ I+ EV I A L GIHTHND+E AVA SL AV G Q+QGT+NG GERCG Sbjct: 185 DVGRIVAEV---IAAGLPGDHLGIHTHNDTENAVACSLAAVDAGARQIQGTLNGLGERCG 241 Query: 241 NANLCSIIPALKLKMKREC-----IGDDQLRKLRDLSRFVYELANLSPNKHQAYVGNSAF 295 NANL ++IP L LK + + L L LSR + E+ N P K AYVG SAF Sbjct: 242 NANLTTLIPTLLLKPPYADQFDIGVSHEGLSTLTALSRMLDEILNRVPTKQAAYVGASAF 301 Query: 296 AHKGGVHVSAIQRHPETYEHLRPELVGNMTRVLVSDLSGRSNILAKAEEFNIKMDSKDPV 355 AHK G+H SAI + P TYEH+ P LVGN + +S+ +G+SN+ + E +++++ DP Sbjct: 302 AHKAGLHASAILKDPSTYEHIDPALVGNARIIPMSNQAGQSNLRRRLSEAGLRVENGDPA 361 Query: 356 TLEILENIKEMENRGYQFEGAEASFELLMKRALGTHRKFFSVIGFRVIDEKR---HEDQK 412 ILE IK E GY ++ A+ASFE+L + LG FF V ++V E+R ++ Sbjct: 362 LARILERIKTREAEGYSYDTAQASFEILAREELGQLPSFFEVKRYKVTVERRKNKYDRMV 421 Query: 413 PLSEATIMVKVGGK--------IEHTAAEGNGPVNALDNALRKALEKFYPRLKEVKLLDY 464 LSEA ++VKV G+ ++ T ++ GPVNAL AL K L ++ L +++L+D+ Sbjct: 422 SLSEAVVVVKVDGQKLLSVSESLDETGSD-RGPVNALAKALTKDLGQYSKALDDMRLVDF 480 Query: 465 KVRVLPAGQGTASSIRVLIESGDKES-RWGTVGVSENIVDASYQALLDSVEYKLHKSEEI 523 KVR+ GT + RV+I+S D RW TVGVS NI+DAS++ALLD++ +KL + + Sbjct: 481 KVRITQG--GTEAVTRVIIDSEDGAGRRWSTVGVSANIIDASFEALLDAIRWKLLRDTDA 538 Query: 524 EG 525 G Sbjct: 539 GG 540 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: 692 Number of extensions: 30 Number of successful extensions: 7 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: 543 Length adjustment: 35 Effective length of query: 493 Effective length of database: 508 Effective search space: 250444 Effective search space used: 250444 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 GFF1624 PGA1_c16460 (2-isopropylmalate synthase/homocitrate synthase-like protein)
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.10766.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.9e-184 599.1 0.0 3.6e-184 598.8 0.0 1.0 1 lcl|FitnessBrowser__Phaeo:GFF1624 PGA1_c16460 2-isopropylmalate sy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF1624 PGA1_c16460 2-isopropylmalate synthase/homocitrate synthase-like protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 598.8 0.0 3.6e-184 3.6e-184 2 522 .. 6 537 .. 5 540 .. 0.94 Alignments for each domain: == domain 1 score: 598.8 bits; conditional E-value: 3.6e-184 TIGR00977 2 lklydttlrdGaqaeGvslsledkiriaeklddlGihyieGGwpganpkdvaffekvkeenlknakvvafsstrrp 77 l+lydttlrdG q++Gv +s ++k++ia +ld lG++yieGGwpganp d ff ++ + +a ++af+ t+r lcl|FitnessBrowser__Phaeo:GFF1624 6 LYLYDTTLRDGQQTQGVQFSTTEKVQIATALDGLGVDYIEGGWPGANPTDSGFFDAAPR---TRATMTAFGMTKRA 78 89****************************************************98755...6899********** PP TIGR00977 78 dkkveedkqlqalikaetpvvtifGkswdlhveealkttleenlkmiydtveylkrfadeviydaehffdGykanp 153 + e+d l a+++a+t v + Gks d hv++al tleenl+ i ++++l +++e ++daehffdGyk np lcl|FitnessBrowser__Phaeo:GFF1624 79 GRSAENDDVLAAVLNAGTAAVCLVGKSHDYHVTHALGITLEENLDNIRASIAHLVAQGREALFDAEHFFDGYKDNP 154 **************************************************************************** PP TIGR00977 154 eyalktlkvaekaGadwlvladtnGGtlpheieeitkkvk.krlkdpqlGihahndsetavansllaveaGavqvq 228 +yal++ ++a +aGa w+vl+dtnGGtlp+++ i+ +v l +lGih+hnd+e ava sl+av aGa+q+q lcl|FitnessBrowser__Phaeo:GFF1624 155 DYALAACRAALEAGARWVVLCDTNGGTLPGDVGRIVAEVIaAGLPGDHLGIHTHNDTENAVACSLAAVDAGARQIQ 230 ***********************************9998615689999**************************** PP TIGR00977 229 GtinGlGercGnanlcslipnlqlkl....gldv.iekenlkkltevarlvaeivnlaldenmpyvGesafahkGG 299 Gt+nGlGercGnanl +lip l lk ++d+ + +e l lt ++r++ ei n+ +++++ yvG safahk G lcl|FitnessBrowser__Phaeo:GFF1624 231 GTLNGLGERCGNANLTTLIPTLLLKPpyadQFDIgVSHEGLSTLTALSRMLDEILNRVPTKQAAYVGASAFAHKAG 306 *************************7222245666899************************************** PP TIGR00977 300 vhvsavkrnpktyehidpelvGnkrkivvselaGksnvleklkelGieidekspkvrkilkkikelekqGyhfeaa 375 +h+sa+ ++p tyehidp lvGn r+i +s++aG+sn+ ++l e G+ +++ +p++ +il++ik e++Gy +++a lcl|FitnessBrowser__Phaeo:GFF1624 307 LHASAILKDPSTYEHIDPALVGNARIIPMSNQAGQSNLRRRLSEAGLRVENGDPALARILERIKTREAEGYSYDTA 382 **************************************************************************** PP TIGR00977 376 easlellvrdalGkrkkyfevdgfrvliakrrdee..slseaeatvrvsvegae.......eltaaeGnGpvsald 442 +as+e+l r+ lG+ ++fev+ ++v++++r+++ +s +ea v v v+g++ ++ Gpv+al lcl|FitnessBrowser__Phaeo:GFF1624 383 QASFEILAREELGQLPSFFEVKRYKVTVERRKNKYdrMVSLSEAVVVVKVDGQKllsvsesLDETGSDRGPVNALA 458 ***************************998877544467777788888888998455554444455568******* PP TIGR00977 443 ralrkalekfypslkdlkltdykvrilnesaGtsaktrvliessdGk.rrwgtvGvseniieasytallesieykl 517 +al k l ++ l d++l+d+kvri + Gt+a trv+i+s dG rrw+tvGvs nii+as+ all++i +kl lcl|FitnessBrowser__Phaeo:GFF1624 459 KALTKDLGQYSKALDDMRLVDFKVRIT--QGGTEAVTRVIIDSEDGAgRRWSTVGVSANIIDASFEALLDAIRWKL 532 **************************7..579*************9659*************************** PP TIGR00977 518 rkdee 522 +d+ lcl|FitnessBrowser__Phaeo:GFF1624 533 LRDTD 537 99975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (526 nodes) Target sequences: 1 (543 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: 00:00:00.02 # Mc/sec: 11.18 // [ok]
This GapMind analysis is from Apr 09 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