Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate 6938908 Sama_3011 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >FitnessBrowser__SB2B:6938908 Length = 404 Score = 536 bits (1381), Expect = e-157 Identities = 258/394 (65%), Positives = 315/394 (79%) Query: 10 RADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTE 69 RA FD+VMVPNYAPAA IPVRG GSRVWDQ G E +DFAGGIAVN LGH HPALV AL E Sbjct: 9 RAQFDEVMVPNYAPAAVIPVRGEGSRVWDQQGTEYVDFAGGIAVNCLGHCHPALVGALKE 68 Query: 70 QANKLWHVSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLARRVAHDRFGT 129 Q KLWH+SN TNEPAL LA KLV+ATFA+RV+F NSGAEANEAA KLARR A ++FG Sbjct: 69 QGEKLWHLSNTMTNEPALALATKLVEATFADRVYFANSGAEANEAALKLARRYAIEKFGE 128 Query: 130 EKYEIVAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALKAAVSDKTCA 189 K E++A +FHGRT FTV+VGGQ+ YSDGFGPK ITH+P+ND+AAL+AAVSD TCA Sbjct: 129 HKVEVIAFDKAFHGRTFFTVSVGGQAAYSDGFGPKPAAITHLPFNDIAALEAAVSDNTCA 188 Query: 190 VVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPD 249 ++LEP+QGEGG++ + +L+ R L D HNAL++FDEVQTG+GR+G L+AY + PD Sbjct: 189 IMLEPLQGEGGIINGDPEFLRAVRRLADKHNALVIFDEVQTGVGRTGDLYAYMGTEIVPD 248 Query: 250 ILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLN 309 ILT+AK+LGGGFPIAAMLTT D+A HL VGTHG+TYGGNPLACA+ AV+DV+NTPEVL+ Sbjct: 249 ILTTAKALGGGFPIAAMLTTADIASHLKVGTHGSTYGGNPLACAIGNAVMDVVNTPEVLD 308 Query: 310 GVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNAAEREGLMIL 369 GV + F+ L QI EKY +F+E+RG GLLLG VL++ + G+++D NA+ EGL+ L Sbjct: 309 GVKHREQLFRDGLAQINEKYHVFSEIRGKGLLLGAVLNEQFAGRSRDFLNASVAEGLLTL 368 Query: 370 QAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKL 403 AG +V+RF PSLV+ +ADI GL RFERA AK+ Sbjct: 369 MAGANVVRFTPSLVIPEADIVEGLARFERAVAKV 402 Lambda K H 0.320 0.136 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: 501 Number of extensions: 8 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
Align candidate 6938908 Sama_3011 (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.carbon/TIGR03246.hmm # target sequence database: /tmp/gapView.21919.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.5e-212 689.8 1.5 6.2e-212 689.7 1.5 1.0 1 lcl|FitnessBrowser__SB2B:6938908 Sama_3011 bifunctional N-succiny Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6938908 Sama_3011 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine t # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 689.7 1.5 6.2e-212 6.2e-212 2 396 .. 8 402 .. 7 403 .. 1.00 Alignments for each domain: == domain 1 score: 689.7 bits; conditional E-value: 6.2e-212 TIGR03246 2 eresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlgngytnep 78 +r++fdevmvp+yapa++ipvrgeGsrvwdq+g ey+dfaGGiavn+lGh+hp+lv alkeq+eklwhl+n++tnep lcl|FitnessBrowser__SB2B:6938908 8 TRAQFDEVMVPNYAPAAVIPVRGEGSRVWDQQGTEYVDFAGGIAVNCLGHCHPALVGALKEQGEKLWHLSNTMTNEP 84 89*************************************************************************** PP TIGR03246 79 vlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftvsvGGqakysedfa 155 +l+la klv+atfad+v+f+nsGaeaneaalklar++a++k+g++k e++af ++fhGrt+ftvsvGGqa+ys++f+ lcl|FitnessBrowser__SB2B:6938908 85 ALALATKLVEATFADRVYFANSGAEANEAALKLARRYAIEKFGEHKVEVIAFDKAFHGRTFFTVSVGGQAAYSDGFG 161 ***************************************************************************** PP TIGR03246 156 plpegikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhnallifdevqtGvGrtGely 232 p+p+ i+h+++nd++al+a++sd+tca+++ep+qGegG+++ d++fl+++r+l d+hnal+ifdevqtGvGrtG+ly lcl|FitnessBrowser__SB2B:6938908 162 PKPAAITHLPFNDIAALEAAVSDNTCAIMLEPLQGEGGIINGDPEFLRAVRRLADKHNALVIFDEVQTGVGRTGDLY 238 ***************************************************************************** PP TIGR03246 233 aymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnplacavaekvldlvntaelleGvkqrhe 309 aym + ++pdilt+akalGgGfpi a+ltt ++a++lkvGthG+tyGGnplaca+ ++v+d+vnt+e+l+Gvk+r++ lcl|FitnessBrowser__SB2B:6938908 239 AYMGTEIVPDILTTAKALGGGFPIAAMLTTADIASHLKVGTHGSTYGGNPLACAIGNAVMDVVNTPEVLDGVKHREQ 315 ***************************************************************************** PP TIGR03246 310 lfvdelekinarykvfseirGkGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfapslvieeeeikeGl 386 lf d l++in++y+vfseirGkGll+Gavl+e++aG+++d++na+ +eG+l l+aG++vvrf+pslvi+e++i eGl lcl|FitnessBrowser__SB2B:6938908 316 LFRDGLAQINEKYHVFSEIRGKGLLLGAVLNEQFAGRSRDFLNASVAEGLLTLMAGANVVRFTPSLVIPEADIVEGL 392 ***************************************************************************** PP TIGR03246 387 arlekavekl 396 ar+e+av+k+ lcl|FitnessBrowser__SB2B:6938908 393 ARFERAVAKV 402 *******987 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.86 // [ok]
This GapMind analysis is from Sep 17 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