Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 6937472 Sama_1628 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >FitnessBrowser__SB2B:6937472 Length = 405 Score = 534 bits (1375), Expect = e-156 Identities = 261/402 (64%), Positives = 314/402 (78%) Query: 5 ITRSNFDEWMMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKAL 64 I RS FDE M+P YAP+ IPV+G GSRLWDQQG+E+IDFAGGIAVN LGH HP LV AL Sbjct: 3 INRSLFDEVMVPNYAPSPIIPVKGLGSRLWDQQGREFIDFAGGIAVNCLGHCHPALVSAL 62 Query: 65 TEQAGKFWHTGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRF 124 TEQA K WH N TNEP L LAK L+D TFA++V+F NSGAEANEAALKL R+ A ++F Sbjct: 63 TEQAQKLWHLSNTMTNEPALMLAKHLVDNTFAEKVYFANSGAEANEAALKLVRRVALNKF 122 Query: 125 GSEKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALIDDNT 184 G++KS I+AFK FHGRTLFTVS GGQPAYS F P P I HA YN+LDS KALI D T Sbjct: 123 GADKSQIIAFKQGFHGRTLFTVSVGGQPAYSDGFGPKPADIDHAEYNNLDSLKALISDRT 182 Query: 185 CAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVT 244 CAV++EP+QGEGG++ +F++G+RELCD HNALL+FDEVQTGVGRTGELYAYM GVT Sbjct: 183 CAVVLEPLQGEGGIINPTPEFIKGVRELCDQHNALLVFDEVQTGVGRTGELYAYMGLGVT 242 Query: 245 PDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREV 304 PD+L+TAKALGGGFPIGA+L + A + VGTHG+TYGGNPLACAV F T+NT EV Sbjct: 243 PDVLTTAKALGGGFPIGAMLTTTELAKHLVVGTHGSTYGGNPLACAVGLAAFTTVNTPEV 302 Query: 305 LNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEEGLM 364 LNGVK+R Q F + LNAIN +Y +F E+RG GLL+G L +YAGKA+ AAEEG++ Sbjct: 303 LNGVKEREQLFRDGLNAINDKYQVFTEVRGKGLLLGAALNADYAGKARDFMLAAAEEGVL 362 Query: 365 ILIAGANVVRFAPALIISEDEVNSGLDRFELACKRFLAGVSS 406 +L+AG NVVRFAP+LII E +V GL RF+ A + +A +++ Sbjct: 363 LLMAGQNVVRFAPSLIIPEADVREGLARFDAAIAKLVARLNA 404 Lambda K H 0.321 0.137 0.412 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: 17 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: 405 Length adjustment: 31 Effective length of query: 375 Effective length of database: 374 Effective search space: 140250 Effective search space used: 140250 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 6937472 Sama_1628 (bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq))
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.3692479.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-216 704.3 0.2 2.6e-216 704.1 0.2 1.0 1 FitnessBrowser__SB2B:6937472 Domain annotation for each sequence (and alignments): >> FitnessBrowser__SB2B:6937472 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 704.1 0.2 2.6e-216 2.6e-216 1 397 [] 3 399 .. 3 399 .. 1.00 Alignments for each domain: == domain 1 score: 704.1 bits; conditional E-value: 2.6e-216 TIGR03246 1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlgngytnepvlr 81 ++r+ fdevmvp+yap+++ipv+g Gsr+wdq+g+e+idfaGGiavn+lGh+hp+lv+al+eqa+klwhl+n++tnep+l FitnessBrowser__SB2B:6937472 3 INRSLFDEVMVPNYAPSPIIPVKGLGSRLWDQQGREFIDFAGGIAVNCLGHCHPALVSALTEQAQKLWHLSNTMTNEPALM 83 78******************************************************************************* PP TIGR03246 82 lakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftvsvGGqakysedfaplpegik 162 lak+lvd+tfa+kv+f+nsGaeaneaalkl r+val+k+ga+ks+i+afk++fhGrtlftvsvGGq++ys++f+p+p++i+ FitnessBrowser__SB2B:6937472 84 LAKHLVDNTFAEKVYFANSGAEANEAALKLVRRVALNKFGADKSQIIAFKQGFHGRTLFTVSVGGQPAYSDGFGPKPADID 164 ********************************************************************************* PP TIGR03246 163 haayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhnallifdevqtGvGrtGelyaymeyGvtpdi 243 ha+yn+l++lkalisd+tcav++ep+qGegG+++++++f+kg+relcd+hnall+fdevqtGvGrtGelyaym +Gvtpd+ FitnessBrowser__SB2B:6937472 165 HAEYNNLDSLKALISDRTCAVVLEPLQGEGGIINPTPEFIKGVRELCDQHNALLVFDEVQTGVGRTGELYAYMGLGVTPDV 245 ********************************************************************************* PP TIGR03246 244 ltsakalGgGfpiGalltteelakvlkvGthGttyGGnplacavaekvldlvntaelleGvkqrhelfvdelekinarykv 324 lt+akalGgGfpiGa+ltt+elak+l vGthG+tyGGnplacav + + +vnt+e+l+Gvk+r++lf d l++in++y+v FitnessBrowser__SB2B:6937472 246 LTTAKALGGGFPIGAMLTTTELAKHLVVGTHGSTYGGNPLACAVGLAAFTTVNTPEVLNGVKEREQLFRDGLNAINDKYQV 326 ********************************************************************************* PP TIGR03246 325 fseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfapslvieeeeikeGlarlekaveklv 397 f+e+rGkGll+Ga+l+++yaGka+d++ aaaeeGvl+l+aG +vvrfapsl+i+e+++ eGlar++ a++klv FitnessBrowser__SB2B:6937472 327 FTEVRGKGLLLGAALNADYAGKARDFMLAAAEEGVLLLMAGQNVVRFAPSLIIPEADVREGLARFDAAIAKLV 399 *********************************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (397 nodes) Target sequences: 1 (405 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: 00:00:00.01 # Mc/sec: 15.47 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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