Align Homocitrate synthase; EC 2.3.3.14 (characterized)
to candidate AZOBR_RS05495 AZOBR_RS05495 homocitrate synthase
Query= SwissProt::P05342 (385 letters) >FitnessBrowser__azobra:AZOBR_RS05495 Length = 381 Score = 424 bits (1091), Expect = e-123 Identities = 224/366 (61%), Positives = 270/366 (73%), Gaps = 1/366 (0%) Query: 3 SVIIDDTTLRDGEQSAGVAFNADEKIAIARALAELGVPELEIGIPSMGEEEREVMHAIAG 62 S II+DTTLRDGEQ+AGVAF DEKIAIARAL E GVPELEIGIP+MG EERE + A+A Sbjct: 6 STIINDTTLRDGEQTAGVAFTLDEKIAIARALDEAGVPELEIGIPAMGPEEREGIRAVAA 65 Query: 63 LGLSSRLLAWCRLCDVDLAAARSTGVTMVDLSLPVSDLMLHHKLNRDRDWALREVARLVG 122 LGL +RL+ WCR+ D DL AA V V+LS+PVSD+ + KL R R WAL E+ R V Sbjct: 66 LGLKARLMVWCRMHDTDLKAALDCKVGTVNLSMPVSDIHITKKLKRSRAWALAEIERKVK 125 Query: 123 EARMAGLEVCLGCEDASRADLEFVVQVGEVAQAAGARRLRFADTVGVMEPFGMLDRFRFL 182 AR GLEV LG ED+SRAD++F++ VAQ AGARR RFADT+GV++PF L Sbjct: 126 TARDHGLEVSLGGEDSSRADMDFLIAAATVAQEAGARRFRFADTLGVLDPFQTRACIERL 185 Query: 183 SRRLDMELEVHAHDDFGLATANTLAAVMGGATHINTTVNGLGERAGNAALEECVLALKNL 242 R D+E+E+HAHDD GLA AN+LAAV+GGATH+NTTVNGLGERAGNA LEE V++LK L Sbjct: 186 RRATDLEIEIHAHDDLGLANANSLAAVLGGATHVNTTVNGLGERAGNAPLEEVVVSLKVL 245 Query: 243 HGIDTGIDTRGIPAISALVERASGRQVAWQKSVVGAGVFTHEAGIHVDGLLKHRRNYEGL 302 +G D G+DTR + AIS LVERAS R VA KS+VG VFTHEAGIHVDGLL+ R Y+ Sbjct: 246 YGQDCGVDTRALGAISDLVERASNRPVAVNKSIVGDAVFTHEAGIHVDGLLRDRATYQNF 305 Query: 303 NPDELGRSHSLVLGKHSGAHMVRNTYRDLGIELADWQSQALLGRIRAFSTRTKRRSPQPA 362 +P E+GR H +VLGKHSG V+ Y LGI D +QA+L R+RA +TR K R+P Sbjct: 306 DPAEVGREHRIVLGKHSGTAGVKMAYGQLGIPCDDATAQAVLPRVRALATRAK-RAPTAE 364 Query: 363 ELQDFY 368 EL+ F+ Sbjct: 365 ELRAFH 370 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: 447 Number of extensions: 13 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 AZOBR_RS05495 AZOBR_RS05495 (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.29425.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-165 536.4 5.4 2.3e-165 536.2 5.4 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS05495 AZOBR_RS05495 homocitrate syntha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS05495 AZOBR_RS05495 homocitrate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 536.2 5.4 2.3e-165 2.3e-165 2 364 .. 7 369 .. 6 370 .. 0.99 Alignments for each domain: == domain 1 score: 536.2 bits; conditional E-value: 2.3e-165 TIGR02660 2 vlinDttLRDGEqaagvaFsaeEKlaiAkaLdeaGvdelEvGipamgeeEraairaiaalglkarllaW 70 +inDttLRDGEq+agvaF+ +EK+aiA+aLdeaGv+elE+Gipamg eEr+ ira+aalglkarl++W lcl|FitnessBrowser__azobra:AZOBR_RS05495 7 TIINDTTLRDGEQTAGVAFTLDEKIAIARALDEAGVPELEIGIPAMGPEEREGIRAVAALGLKARLMVW 75 589****************************************************************** PP TIGR02660 71 cRlraedieaaaevGvkavdlsvpvsdlqleaklkkdrawvleelkelvslakeeglkvsvgaeDasRa 139 cR++++d++aa ++ v +v+ls+pvsd+++++klk++raw+l+e+++ v++a+++gl+vs+g+eD+sRa lcl|FitnessBrowser__azobra:AZOBR_RS05495 76 CRMHDTDLKAALDCKVGTVNLSMPVSDIHITKKLKRSRAWALAEIERKVKTARDHGLEVSLGGEDSSRA 144 ********************************************************************* PP TIGR02660 140 deeflvelaevakeagakRlRfaDtvgvldPfstyelvkalraalelelElHaHnDlGlAtAntlaavk 208 d++fl++ a+va+eaga+R+RfaDt+gvldPf+t + +++lr+a++le+E+HaH+DlGlA An+laav lcl|FitnessBrowser__azobra:AZOBR_RS05495 145 DMDFLIAAATVAQEAGARRFRFADTLGVLDPFQTRACIERLRRATDLEIEIHAHDDLGLANANSLAAVL 213 ********************************************************************* PP TIGR02660 209 aGassvsvtvlGlGERAGnAaleevalalkellgldtgidlselkelsqlvakasgraleaqkavvGes 277 +Ga++v++tv+GlGERAGnA+leev+++lk l+g+d+g+d+++l ++s+lv++as+r+++++k++vG++ lcl|FitnessBrowser__azobra:AZOBR_RS05495 214 GGATHVNTTVNGLGERAGNAPLEEVVVSLKVLYGQDCGVDTRALGAISDLVERASNRPVAVNKSIVGDA 282 ********************************************************************* PP TIGR02660 278 vFaHEsGiHvdgllkdeatYesldPeevGrerelviGKHsgraaviealkelgleleeeeaeelleavr 346 vF+HE+GiHvdgll+d+atY+++dP+evGre+++v+GKHsg+a+v+ a+ +lg++ ++++a+++l++vr lcl|FitnessBrowser__azobra:AZOBR_RS05495 283 VFTHEAGIHVDGLLRDRATYQNFDPAEVGREHRIVLGKHSGTAGVKMAYGQLGIPCDDATAQAVLPRVR 351 ********************************************************************* PP TIGR02660 347 avaerlKrsleeeelaal 364 a a+r+Kr++++eel+a+ lcl|FitnessBrowser__azobra:AZOBR_RS05495 352 ALATRAKRAPTAEELRAF 369 ***************986 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: 11.91 // [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