Align homocitrate synthase (EC 2.3.3.14) (characterized)
to candidate WP_011383972.1 AMB_RS07875 homocitrate synthase
Query= BRENDA::A0A1Y6KBA1 (416 letters) >NCBI__GCF_000009985.1:WP_011383972.1 Length = 381 Score = 397 bits (1019), Expect = e-115 Identities = 203/352 (57%), Positives = 259/352 (73%) Query: 41 VILNDTTLRDGEQAPGVAFALSEKVAIARALARAGVPEIEAGTPAMGADEISAIRAIVEA 100 +++NDTTLRDGEQ GVAF L EK+ IAR L AGVPEIE G PAMGA+E +AIR + Sbjct: 7 IVMNDTTLRDGEQTAGVAFRLDEKLDIARTLDIAGVPEIEVGIPAMGAEEQAAIRKVAGL 66 Query: 101 GLPATIIGWCRMREADVDAAIAAGVSMVNVSIPTSDVQIAAKLGGGRSVALELLKRVVSY 160 GL A +I WCRM E D++AA V+ VN+SIP SD+Q+AAK+G R+ ALE ++ +V Sbjct: 67 GLKARLIAWCRMMEDDLEAAALCDVATVNLSIPVSDLQLAAKMGRDRAWALEHIRVMVGK 126 Query: 161 ARSRGLGVAVGGEDSSRADVGFLAEVIATAKALGARRFRVADTLSVLDPDATSALVGALR 220 AR+ G V VGGEDSSRAD FLA+V+ +A GA+RFR ADT+ ++DP A ALR Sbjct: 127 ARAMGFDVLVGGEDSSRADPAFLADVVRACEAAGAQRFRFADTMGIMDPFAVHDAFRALR 186 Query: 221 ATTDLEIEFHGHDDLGLATANTLAAIKAGATHASVTVIGLGERAGNAPLEEVAVALRQLY 280 A T +E+E H HDDLGLATAN+LAA++ GATH S TV GLGERAGNAPLEEV VAL LY Sbjct: 187 AATSMELEIHAHDDLGLATANSLAAVRGGATHVSTTVNGLGERAGNAPLEEVVVALGHLY 246 Query: 281 RRETGIVLAELDHVANVVAAAAARAIPLNKAIVGEHVFTHESGIHVDGLLKDQRTYQALD 340 RETGI +L V+ +VA A+ R +P++K+IVGE++FTHESGIHV GLL+D RTYQALD Sbjct: 247 GRETGIDKRQLGRVSKLVAEASGRPVPVDKSIVGENIFTHESGIHVSGLLRDPRTYQALD 306 Query: 341 PMLFGRSNRIVIGKHSGLSAITSLLSDLRLPASADQAQRILARVRKHAVAHK 392 P GR +R+V+GKHSGL+++ ++ L A +A+ +LA+VR+HA K Sbjct: 307 PAELGRGHRLVLGKHSGLTSVLHACREIGLEVDAAKARAMLAQVRRHASTTK 358 Lambda K H 0.317 0.132 0.369 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: 471 Number of extensions: 28 Number of successful extensions: 1 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: 416 Length of database: 381 Length adjustment: 31 Effective length of query: 385 Effective length of database: 350 Effective search space: 134750 Effective search space used: 134750 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: 50 (23.9 bits)
Align candidate WP_011383972.1 AMB_RS07875 (homocitrate synthase)
to HMM TIGR02660 (nifV: homocitrate synthase (EC 2.3.3.14))
# 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/TIGR02660.hmm # target sequence database: /tmp/gapView.14104.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02660 [M=365] Accession: TIGR02660 Description: nifV_homocitr: homocitrate 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.8e-160 517.9 6.6 1e-159 517.7 6.6 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011383972.1 AMB_RS07875 homocitrate synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011383972.1 AMB_RS07875 homocitrate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 517.7 6.6 1e-159 1e-159 2 364 .. 7 369 .. 6 370 .. 0.99 Alignments for each domain: == domain 1 score: 517.7 bits; conditional E-value: 1e-159 TIGR02660 2 vlinDttLRDGEqaagvaFsaeEKlaiAkaLdeaGvdelEvGipamgeeEraairaiaalglkarllaW 70 +++nDttLRDGEq+agvaF+ +EKl iA+ Ld aGv+e+EvGipamg+eE+aair++a lglkarl+aW lcl|NCBI__GCF_000009985.1:WP_011383972.1 7 IVMNDTTLRDGEQTAGVAFRLDEKLDIARTLDIAGVPEIEVGIPAMGAEEQAAIRKVAGLGLKARLIAW 75 799****************************************************************** PP TIGR02660 71 cRlraedieaaaevGvkavdlsvpvsdlqleaklkkdrawvleelkelvslakeeglkvsvgaeDasRa 139 cR+ + d+eaaa + v++v+ls+pvsdlql+ak+ +draw+le+++ +v +a+ +g +v vg+eD+sRa lcl|NCBI__GCF_000009985.1:WP_011383972.1 76 CRMMEDDLEAAALCDVATVNLSIPVSDLQLAAKMGRDRAWALEHIRVMVGKARAMGFDVLVGGEDSSRA 144 ********************************************************************* PP TIGR02660 140 deeflvelaevakeagakRlRfaDtvgvldPfstyelvkalraalelelElHaHnDlGlAtAntlaavk 208 d++fl+++++ ++aga+R+RfaDt+g++dPf+++++++alraa+++elE+HaH+DlGlAtAn+laav+ lcl|NCBI__GCF_000009985.1:WP_011383972.1 145 DPAFLADVVRACEAAGAQRFRFADTMGIMDPFAVHDAFRALRAATSMELEIHAHDDLGLATANSLAAVR 213 ********************************************************************* PP TIGR02660 209 aGassvsvtvlGlGERAGnAaleevalalkellgldtgidlselkelsqlvakasgraleaqkavvGes 277 +Ga++vs+tv+GlGERAGnA+leev++al +l+g++tgid ++l ++s+lva+asgr+++++k++vGe+ lcl|NCBI__GCF_000009985.1:WP_011383972.1 214 GGATHVSTTVNGLGERAGNAPLEEVVVALGHLYGRETGIDKRQLGRVSKLVAEASGRPVPVDKSIVGEN 282 ********************************************************************* PP TIGR02660 278 vFaHEsGiHvdgllkdeatYesldPeevGrerelviGKHsgraaviealkelgleleeeeaeelleavr 346 +F+HEsGiHv+gll+d++tY++ldP+e+Gr ++lv+GKHsg ++v +a++e+gle+++++a+++l++vr lcl|NCBI__GCF_000009985.1:WP_011383972.1 283 IFTHESGIHVSGLLRDPRTYQALDPAELGRGHRLVLGKHSGLTSVLHACREIGLEVDAAKARAMLAQVR 351 ********************************************************************* PP TIGR02660 347 avaerlKrsleeeelaal 364 ++a+++K +++++l+++ lcl|NCBI__GCF_000009985.1:WP_011383972.1 352 RHASTTKTIPTADDLRRF 369 **************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (365 nodes) Target sequences: 1 (381 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 10.71 // [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