Align Homocitrate synthase; EC 2.3.3.14 (characterized)
to candidate WP_011813096.1 HHAL_RS01440 homocitrate synthase
Query= SwissProt::P05342 (385 letters) >NCBI__GCF_000015585.1:WP_011813096.1 Length = 381 Score = 423 bits (1088), Expect = e-123 Identities = 225/365 (61%), Positives = 270/365 (73%), Gaps = 1/365 (0%) Query: 1 MASVIIDDTTLRDGEQSAGVAFNADEKIAIARALAELGVPELEIGIPSMGEEEREVMHAI 60 MA V+IDDTTLRDGEQSAGVAF EK+AIA AL +GVPELE+GIP+MG EER + A+ Sbjct: 1 MAGVVIDDTTLRDGEQSAGVAFTRAEKLAIAAALDRIGVPELEVGIPAMGPEERADIRAL 60 Query: 61 AGLGLSSRLLAWCRLCDVDLAAARSTGVTMVDLSLPVSDLMLHHKLNRDRDWALREVARL 120 A G+S+RLL W R+ + DL A GV VD S+PVSD + HKL RDR W L + Sbjct: 61 AESGVSARLLVWARMRETDLQACGGLGVWGVDGSIPVSDQQIAHKLGRDRRWVLGRIDAW 120 Query: 121 VGEARMAGLEVCLGCEDASRADLEFVVQVGEVAQAAGARRLRFADTVGVMEPFGMLDRFR 180 V AR+ GLEV +G EDA+RAD EF+V+V A+AAGARRLR ADTVG+ EPF + + F+ Sbjct: 121 VRRARVQGLEVSVGGEDATRADPEFLVEVARCAEAAGARRLRIADTVGIAEPFAVCEVFQ 180 Query: 181 FLSRRLDMELEVHAHDDFGLATANTLAAVMGGATHINTTVNGLGERAGNAALEECVLALK 240 L D+ELE+HAHDDFGLATAN+LAAV GGATH+NTTV GLGERAGNAALEE VL L Sbjct: 181 RLRAATDLELEMHAHDDFGLATANSLAAVRGGATHVNTTVCGLGERAGNAALEEVVLGLH 240 Query: 241 NLHGIDTGIDTRGIPAISALVERASGRQVAWQKSVVGAGVFTHEAGIHVDGLLKHRRNYE 300 L TG+DT G+ A++ALVE ASGR V W KSVVGAGVF HEAGIHVDGLLK RNY+ Sbjct: 241 RLCHRPTGVDTAGLTAVAALVEAASGRPVPWGKSVVGAGVFRHEAGIHVDGLLKDARNYQ 300 Query: 301 GLNPDELGRSHSLVLGKHSGAHMVRNTYRDLGIELADWQSQALLGRIRAFSTRTKRRSPQ 360 GL+PDE+GR H LVLGKHSG V+ R+ G++L Q++ALL IR +S T +R+P Sbjct: 301 GLDPDEVGRCHELVLGKHSGTRGVQAACREAGVDLDREQARALLPLIRRWSV-THKRAPS 359 Query: 361 PAELQ 365 EL+ Sbjct: 360 ADELR 364 Lambda K H 0.320 0.135 0.396 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: 522 Number of extensions: 22 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: 385 Length of database: 381 Length adjustment: 30 Effective length of query: 355 Effective length of database: 351 Effective search space: 124605 Effective search space used: 124605 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
Align candidate WP_011813096.1 HHAL_RS01440 (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.17168.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-160 520.9 4.0 1.2e-160 520.7 4.0 1.0 1 lcl|NCBI__GCF_000015585.1:WP_011813096.1 HHAL_RS01440 homocitrate synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015585.1:WP_011813096.1 HHAL_RS01440 homocitrate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 520.7 4.0 1.2e-160 1.2e-160 2 364 .. 4 366 .. 3 367 .. 1.00 Alignments for each domain: == domain 1 score: 520.7 bits; conditional E-value: 1.2e-160 TIGR02660 2 vlinDttLRDGEqaagvaFsaeEKlaiAkaLdeaGvdelEvGipamgeeEraairaiaalglkarllaW 70 v+i+DttLRDGEq+agvaF+++EKlaiA+aLd++Gv+elEvGipamg eEra+ira+a+ g +arll+W lcl|NCBI__GCF_000015585.1:WP_011813096.1 4 VVIDDTTLRDGEQSAGVAFTRAEKLAIAAALDRIGVPELEVGIPAMGPEERADIRALAESGVSARLLVW 72 89******************************************************************* PP TIGR02660 71 cRlraedieaaaevGvkavdlsvpvsdlqleaklkkdrawvleelkelvslakeeglkvsvgaeDasRa 139 +R+r++d++a +Gv vd s+pvsd+q+++kl +dr+wvl ++ + v+ a+ +gl+vsvg+eDa+Ra lcl|NCBI__GCF_000015585.1:WP_011813096.1 73 ARMRETDLQACGGLGVWGVDGSIPVSDQQIAHKLGRDRRWVLGRIDAWVRRARVQGLEVSVGGEDATRA 141 ********************************************************************* PP TIGR02660 140 deeflvelaevakeagakRlRfaDtvgvldPfstyelvkalraalelelElHaHnDlGlAtAntlaavk 208 d+eflve+a++a++aga+RlR+aDtvg+ +Pf++ e +++lraa++lelE+HaH+D+GlAtAn+laav+ lcl|NCBI__GCF_000015585.1:WP_011813096.1 142 DPEFLVEVARCAEAAGARRLRIADTVGIAEPFAVCEVFQRLRAATDLELEMHAHDDFGLATANSLAAVR 210 ********************************************************************* PP TIGR02660 209 aGassvsvtvlGlGERAGnAaleevalalkellgldtgidlselkelsqlvakasgraleaqkavvGes 277 +Ga++v++tv GlGERAGnAaleev+l+l++l+++ tg+d+ l+++++lv++asgr++++ k+vvG+ lcl|NCBI__GCF_000015585.1:WP_011813096.1 211 GGATHVNTTVCGLGERAGNAALEEVVLGLHRLCHRPTGVDTAGLTAVAALVEAASGRPVPWGKSVVGAG 279 ********************************************************************* PP TIGR02660 278 vFaHEsGiHvdgllkdeatYesldPeevGrerelviGKHsgraaviealkelgleleeeeaeelleavr 346 vF+HE+GiHvdgllkd+++Y++ldP+evGr +elv+GKHsg+++v++a++e+g++l++e+a++ll+ +r lcl|NCBI__GCF_000015585.1:WP_011813096.1 280 VFRHEAGIHVDGLLKDARNYQGLDPDEVGRCHELVLGKHSGTRGVQAACREAGVDLDREQARALLPLIR 348 ********************************************************************* PP TIGR02660 347 avaerlKrsleeeelaal 364 +++ ++Kr+++++el+al lcl|NCBI__GCF_000015585.1:WP_011813096.1 349 RWSVTHKRAPSADELRAL 366 ***************997 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.68 // [ok]
This GapMind analysis is from Apr 10 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