Align succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_043529620.1 JH15_RS09230 aspartate aminotransferase family protein
Query= BRENDA::O30508 (406 letters) >NCBI__GCF_000759345.1:WP_043529620.1 Length = 404 Score = 527 bits (1357), Expect = e-154 Identities = 248/395 (62%), Positives = 322/395 (81%) Query: 10 RADFDRYMVPNYAPAAFIPVRGEGSRVWDQSGRELIDFAGGIAVTSLGHAHPALVKALTE 69 R+DFD+YM PNY+P IPVRG+GSR+WDQ GRE IDFAGGIAV +LGH HP LV+AL Sbjct: 7 RSDFDQYMAPNYSPQQVIPVRGKGSRLWDQEGREYIDFAGGIAVNALGHCHPVLVEALKT 66 Query: 70 QAQRIWHVSNVFTNEPALRLARKLVDATFAERVFLANSGAEANEAAFKLARRYANDVYGP 129 Q + +WH+SNV+TNEPAL+LA+ LV+ TFA++VFL +SG EANEAA KLARRY + +G Sbjct: 67 QGETLWHLSNVYTNEPALKLAKSLVERTFADKVFLCSSGGEANEAALKLARRYIYEKHGE 126 Query: 130 QKYEIIAASNSFHGRTLFTVNVGGQPKYSDGFGPKFEGITHVPYNDLEALKAAISDKTCA 189 QK +II+ SFHGRT FTV+VGGQPKYS GFGP GI H YNDL++++A I D TCA Sbjct: 127 QKDKIISFRQSFHGRTFFTVSVGGQPKYSQGFGPVPGGIQHAEYNDLDSVRALIDDNTCA 186 Query: 190 VVLEPIQGEGGVLPAQQAYLEGARKLCDEHNALLVFDEVQSGMGRVGELFAYMHYGVVPD 249 +++EP+QGEGG++PA Q +L G R+LCD+H ALL+FDEVQ+G+GR G+ FAYMHYGV PD Sbjct: 187 IMVEPMQGEGGIVPATQEFLSGLRELCDQHQALLIFDEVQTGVGRSGKFFAYMHYGVTPD 246 Query: 250 ILSSAKSLGGGFPIGAMLTTGEIAKHLSVGTHGTTYGGNPLASAVAEAALDVINTPEVLD 309 IL+SAKSLGGGFPIGAMLTT +IA L++GTHG+TYGGN LASAVA AA++ I+TPEVL+ Sbjct: 247 ILTSAKSLGGGFPIGAMLTTDKIAPSLAIGTHGSTYGGNALASAVALAAVEHIDTPEVLE 306 Query: 310 GVKAKHERFKSRLQKIGQEYGIFDEIRGMGLLIGAALTDEWKGKARDVLNAAEKEAVMVL 369 GV+ +H+ F+ L+ I +++G+F EIRGMGLL+GA ++D ++G+A+D+L A +E VM L Sbjct: 307 GVQKRHDLFREHLEAINEKHGVFKEIRGMGLLVGAQMSDAYEGRAKDILPLAIEEGVMAL 366 Query: 370 QASPDVVRFAPSLVIDDAEIDEGLERFERAVAKLV 404 A P+V+R APSLVI +++IDEG+ R RA+ +LV Sbjct: 367 IAGPNVLRLAPSLVIPESDIDEGMTRLARAIDRLV 401 Lambda K H 0.318 0.135 0.394 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: 549 Number of extensions: 16 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: 404 Length adjustment: 31 Effective length of query: 375 Effective length of database: 373 Effective search space: 139875 Effective search space used: 139875 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_043529620.1 JH15_RS09230 (aspartate aminotransferase family protein)
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.carbon/TIGR03246.hmm # target sequence database: /tmp/gapView.2993326.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-213 694.7 0.0 2.1e-213 694.5 0.0 1.0 1 NCBI__GCF_000759345.1:WP_043529620.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000759345.1:WP_043529620.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 694.5 0.0 2.1e-213 2.1e-213 2 397 .] 6 401 .. 5 401 .. 1.00 Alignments for each domain: == domain 1 score: 694.5 bits; conditional E-value: 2.1e-213 TIGR03246 2 eresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlgngy 74 +r++fd++m p+y+p ++ipvrg+Gsr+wdqeg+eyidfaGGiavnalGh+hp lvealk q+e+lwhl+n+y NCBI__GCF_000759345.1:WP_043529620.1 6 TRSDFDQYMAPNYSPQQVIPVRGKGSRLWDQEGREYIDFAGGIAVNALGHCHPVLVEALKTQGETLWHLSNVY 78 699********************************************************************** PP TIGR03246 75 tnepvlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftvsvGGq 147 tnep+l+lak lv+ tfadkvf+c sG+eaneaalklar++ ++k+g++k++i++f++sfhGrt+ftvsvGGq NCBI__GCF_000759345.1:WP_043529620.1 79 TNEPALKLAKSLVERTFADKVFLCSSGGEANEAALKLARRYIYEKHGEQKDKIISFRQSFHGRTFFTVSVGGQ 151 ************************************************************************* PP TIGR03246 148 akysedfaplpegikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhnallifde 220 +kys++f+p+p+gi+ha+yndl++++ali+d+tca++vep+qGegG+vpa+++fl glrelcd+h+allifde NCBI__GCF_000759345.1:WP_043529620.1 152 PKYSQGFGPVPGGIQHAEYNDLDSVRALIDDNTCAIMVEPMQGEGGIVPATQEFLSGLRELCDQHQALLIFDE 224 ************************************************************************* PP TIGR03246 221 vqtGvGrtGelyaymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnplacavaekvld 293 vqtGvGr G+++aym+yGvtpdiltsak+lGgGfpiGa+ltt+++a +l++GthG+tyGGn la+ava + ++ NCBI__GCF_000759345.1:WP_043529620.1 225 VQTGVGRSGKFFAYMHYGVTPDILTSAKSLGGGFPIGAMLTTDKIAPSLAIGTHGSTYGGNALASAVALAAVE 297 ************************************************************************* PP TIGR03246 294 lvntaelleGvkqrhelfvdelekinarykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGp 366 ++t+e+leGv++rh+lf ++le+in+++ vf+eirG+Gll+Ga+++++y+G+akd++ +a eeGv++liaGp NCBI__GCF_000759345.1:WP_043529620.1 298 HIDTPEVLEGVQKRHDLFREHLEAINEKHGVFKEIRGMGLLVGAQMSDAYEGRAKDILPLAIEEGVMALIAGP 370 ************************************************************************* PP TIGR03246 367 dvvrfapslvieeeeikeGlarlekaveklv 397 +v+r+apslvi+e++i+eG++rl++a+ +lv NCBI__GCF_000759345.1:WP_043529620.1 371 NVLRLAPSLVIPESDIDEGMTRLARAIDRLV 401 ***************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (397 nodes) Target sequences: 1 (404 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 18.02 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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