Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate BPHYT_RS07695 BPHYT_RS07695 acetylornithine aminotransferase
Query= reanno::WCS417:GFF4238 (406 letters) >FitnessBrowser__BFirm:BPHYT_RS07695 Length = 411 Score = 508 bits (1309), Expect = e-148 Identities = 240/399 (60%), Positives = 311/399 (77%) Query: 8 VQRADFDQVMVPNYAPAAFIPVRGEGSRVWDQAGRELIDFAGGIAVNVLGHAHPALVGAL 67 V R FD+VMVP ++PAAF+P RG GSRVWD GR+ IDFAGGIAV LGHAHP L+ L Sbjct: 6 VTRQTFDEVMVPVFSPAAFVPDRGLGSRVWDTQGRDYIDFAGGIAVTALGHAHPELLNVL 65 Query: 68 TEQAHKLWHVSNVFTNEPALRLAHKLIDATFAERVFFCNSGAEANEAAFKLARRVAFDRF 127 EQ KLWH+ N +TNEP LRLA +L D TFA+R FF NSGAEANEAA KLARRVAFDR Sbjct: 66 HEQGGKLWHIGNGYTNEPVLRLAKRLEDLTFADRAFFANSGAEANEAALKLARRVAFDRH 125 Query: 128 GSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLDALKAAVSDKT 187 G++KYEII+ SFHGRT FTV+VGGQ KYS+GFGP GITH+PYND++A+K A+ +T Sbjct: 126 GADKYEIISFTQSFHGRTFFTVSVGGQPKYSEGFGPVPAGITHLPYNDIEAVKKAIGAQT 185 Query: 188 CAVVLEPIQGEGGVLPAELAYLQGARDLCDANNALLVFDEVQTGMGRSGHLFAYQHYGVT 247 CAV++EPIQGEGGV+PA+ A+L+ R+ CD + ALL+FDEVQTG+GRSG+ +AYQ GVT Sbjct: 186 CAVIVEPIQGEGGVIPADPAFLKALREACDQHGALLIFDEVQTGVGRSGYFYAYQETGVT 245 Query: 248 PDILTSAKSLGGGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEV 307 PDILT+AK+LG GFPI AMLTT LA + VG HGTTYGGNPL A+AE V+++++ P++ Sbjct: 246 PDILTTAKALGNGFPIGAMLTTNELAAYFKVGVHGTTYGGNPLGAAIAEKVVELVSDPKL 305 Query: 308 LAGVNAKHDLFKARLEQIGKQYGIFTEVRGMGLLLGCVLSDAFKGKAKDVFNAAEKENLM 367 L GV ++ + K L ++ +++G+FTEVRG GLL+G L++AFKG+AKD AA + ++ Sbjct: 306 LEGVRSRSEALKGHLAKLNERFGLFTEVRGRGLLIGAELNEAFKGRAKDFVTAAGQHGVI 365 Query: 368 ILQAGPDVVRFAPSLVVEDADIKEGLDRFERAVKALTQA 406 +L AGPDV+RF PSL++ D+ EG +R +A++++ A Sbjct: 366 MLMAGPDVLRFVPSLIMPLDDMNEGFERLAKAIESIVGA 404 Lambda K H 0.320 0.137 0.400 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: 536 Number of extensions: 15 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: 406 Length of database: 411 Length adjustment: 31 Effective length of query: 375 Effective length of database: 380 Effective search space: 142500 Effective search space used: 142500 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 BPHYT_RS07695 BPHYT_RS07695 (acetylornithine aminotransferase)
to HMM TIGR03246 (astC: succinylornithine transaminase family (EC 2.6.1.81))
# 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/TIGR03246.hmm # target sequence database: /tmp/gapView.6399.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03246 [M=397] Accession: TIGR03246 Description: arg_catab_astC: succinylornithine transaminase family 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-215 700.8 0.1 2.9e-215 700.6 0.1 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS07695 BPHYT_RS07695 acetylornithine am Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS07695 BPHYT_RS07695 acetylornithine aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 700.6 0.1 2.9e-215 2.9e-215 1 397 [] 6 402 .. 6 402 .. 1.00 Alignments for each domain: == domain 1 score: 700.6 bits; conditional E-value: 2.9e-215 TIGR03246 1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhl 70 v+r++fdevmvpv++pa+f+p+rg Gsrvwd++g++yidfaGGiav+alGhahpel ++l+eq+ klwh+ lcl|FitnessBrowser__BFirm:BPHYT_RS07695 6 VTRQTFDEVMVPVFSPAAFVPDRGLGSRVWDTQGRDYIDFAGGIAVTALGHAHPELLNVLHEQGGKLWHI 75 79******************************************************************** PP TIGR03246 71 gngytnepvlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlf 140 gngytnepvlrlak+l d tfad++ff+nsGaeaneaalklar+va+d++ga+k+ei++f++sfhGrt+f lcl|FitnessBrowser__BFirm:BPHYT_RS07695 76 GNGYTNEPVLRLAKRLEDLTFADRAFFANSGAEANEAALKLARRVAFDRHGADKYEIISFTQSFHGRTFF 145 ********************************************************************** PP TIGR03246 141 tvsvGGqakysedfaplpegikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcd 210 tvsvGGq+kyse+f+p+p+gi+h++ynd+ea+k++i +tcavivepiqGegGv+pad+aflk+lre+cd lcl|FitnessBrowser__BFirm:BPHYT_RS07695 146 TVSVGGQPKYSEGFGPVPAGITHLPYNDIEAVKKAIGAQTCAVIVEPIQGEGGVIPADPAFLKALREACD 215 ********************************************************************** PP TIGR03246 211 rhnallifdevqtGvGrtGelyaymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGG 280 +h+allifdevqtGvGr G++yay+e+Gvtpdilt+akalG+GfpiGa+ltt+ela+ +kvG+hGttyGG lcl|FitnessBrowser__BFirm:BPHYT_RS07695 216 QHGALLIFDEVQTGVGRSGYFYAYQETGVTPDILTTAKALGNGFPIGAMLTTNELAAYFKVGVHGTTYGG 285 ********************************************************************** PP TIGR03246 281 nplacavaekvldlvntaelleGvkqrhelfvdelekinarykvfseirGkGlliGavlteeyaGkakdl 350 npl++a+aekv++lv++++lleGv+ r+e + +l+k+n+r+ +f+e+rG+GlliGa+l+e+++G+akd+ lcl|FitnessBrowser__BFirm:BPHYT_RS07695 286 NPLGAAIAEKVVELVSDPKLLEGVRSRSEALKGHLAKLNERFGLFTEVRGRGLLIGAELNEAFKGRAKDF 355 ********************************************************************** PP TIGR03246 351 vnaaaeeGvlvliaGpdvvrfapslvieeeeikeGlarlekaveklv 397 v+aa ++Gv++l+aGpdv+rf psl+++ ++++eG++rl+ka+e++v lcl|FitnessBrowser__BFirm:BPHYT_RS07695 356 VTAAGQHGVIMLMAGPDVLRFVPSLIMPLDDMNEGFERLAKAIESIV 402 *******************************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (397 nodes) Target sequences: 1 (411 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.49 // [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