Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate PfGW456L13_1971 Succinylornithine transaminase (EC 2.6.1.81)
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971 Length = 406 Score = 775 bits (2001), Expect = 0.0 Identities = 386/406 (95%), Positives = 397/406 (97%) Query: 1 MSVEHAAVERADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60 MSVEHAAV+RADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH Sbjct: 1 MSVEHAAVQRADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAH 60 Query: 61 PALVAALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERVFFCNSGAEANEAAFKLAR 120 PALV ALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAER FFCNSGAEANEAAFKLAR Sbjct: 61 PALVGALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERAFFCNSGAEANEAAFKLAR 120 Query: 121 RVAHDRFGTEKYEIVAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180 RVA DR+G+EKYEI+AALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK Sbjct: 121 RVAFDRYGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLAALK 180 Query: 181 AAVSDKTCAVVLEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFA 240 AAVSDKTCAVVLEPIQGEGGVLPAEL+YLQGARELC+ HNALLVFDEVQTGMGR+G LFA Sbjct: 181 AAVSDKTCAVVLEPIQGEGGVLPAELAYLQGARELCNEHNALLVFDEVQTGMGRTGHLFA 240 Query: 241 YQHYGVTPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVID 300 YQHYGV PDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVA AVID Sbjct: 241 YQHYGVIPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAGAVID 300 Query: 301 VINTPEVLNGVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNA 360 VINTPEVL GVNAKHDKFK RLEQIGEKYGLFT+VRGLGLL+GCVLSDAWKGKAKDIFNA Sbjct: 301 VINTPEVLAGVNAKHDKFKARLEQIGEKYGLFTQVRGLGLLIGCVLSDAWKGKAKDIFNA 360 Query: 361 AEREGLMILQAGPDVIRFAPSLVVEDADIDAGLDRFERAAAKLTQA 406 AE+EGLMILQAGPDV+RFAPSLVVEDADIDAGLDRFERAAAKLTQA Sbjct: 361 AEQEGLMILQAGPDVVRFAPSLVVEDADIDAGLDRFERAAAKLTQA 406 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: 657 Number of extensions: 7 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: 406 Length adjustment: 31 Effective length of query: 375 Effective length of database: 375 Effective search space: 140625 Effective search space used: 140625 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 PfGW456L13_1971 (Succinylornithine transaminase (EC 2.6.1.81))
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.23545.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-220 717.9 1.6 1.9e-220 717.7 1.6 1.0 1 lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971 Succinylornithine transaminase ( Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971 Succinylornithine transaminase (EC 2.6.1.81) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 717.7 1.6 1.9e-220 1.9e-220 1 396 [. 8 403 .. 8 404 .. 1.00 Alignments for each domain: == domain 1 score: 717.7 bits; conditional E-value: 1.9e-220 TIGR03246 1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpe 55 v+r++fd+vmvp+yapa+fipvrg Gsrvwdq+g+e+idfaGGiavn lGhahp+ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971 8 VQRADFDQVMVPNYAPAAFIPVRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPA 62 79***************************************************** PP TIGR03246 56 lvealkeqaeklwhlgngytnepvlrlakklvdatfadkvffcnsGaeaneaalk 110 lv al+eqa+klwh++n++tnep+lrla+klvdatfa+++ffcnsGaeaneaa+k lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971 63 LVGALTEQANKLWHVSNVFTNEPALRLAHKLVDATFAERAFFCNSGAEANEAAFK 117 ******************************************************* PP TIGR03246 111 larkvaldkygaekseivafknsfhGrtlftvsvGGqakysedfaplpegikhaa 165 lar+va+d+yg+ek+ei+a nsfhGrtlftv vGGq+kys++f+p+++gi+h++ lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971 118 LARRVAFDRYGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVP 172 ******************************************************* PP TIGR03246 166 yndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhnallifde 220 yndl+alka++sdktcav++epiqGegGv+pa+ a+l+g+relc++hnall+fde lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971 173 YNDLAALKAAVSDKTCAVVLEPIQGEGGVLPAELAYLQGARELCNEHNALLVFDE 227 ******************************************************* PP TIGR03246 221 vqtGvGrtGelyaymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthG 275 vqtG+GrtG+l+ay++yGv+pdiltsak+lGgGfpi a+ltte+lak+l vGthG lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971 228 VQTGMGRTGHLFAYQHYGVIPDILTSAKSLGGGFPIAAMLTTEDLAKHLVVGTHG 282 ******************************************************* PP TIGR03246 276 ttyGGnplacavaekvldlvntaelleGvkqrhelfvdelekinarykvfseirG 330 ttyGGnplacava++v+d++nt+e+l+Gv+++h++f ++le+i+++y +f+++rG lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971 283 TTYGGNPLACAVAGAVIDVINTPEVLAGVNAKHDKFKARLEQIGEKYGLFTQVRG 337 ******************************************************* PP TIGR03246 331 kGlliGavlteeyaGkakdlvnaaaeeGvlvliaGpdvvrfapslvieeeeikeG 385 GlliG+vl+++++Gkakd+ naa++eG+++l+aGpdvvrfapslv+e+++i+ G lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971 338 LGLLIGCVLSDAWKGKAKDIFNAAEQEGLMILQAGPDVVRFAPSLVVEDADIDAG 392 ******************************************************* PP TIGR03246 386 larlekavekl 396 l+r+e+a +kl lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1971 393 LDRFERAAAKL 403 *******9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (397 nodes) Target sequences: 1 (406 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.21 // [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