Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate BWI76_RS11670 BWI76_RS11670 aspartate aminotransferase family protein
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >FitnessBrowser__Koxy:BWI76_RS11670 Length = 406 Score = 818 bits (2113), Expect = 0.0 Identities = 406/406 (100%), Positives = 406/406 (100%) Query: 1 MSQSITRSNFDEWMMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRL 60 MSQSITRSNFDEWMMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRL Sbjct: 1 MSQSITRSNFDEWMMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRL 60 Query: 61 VKALTEQAGKFWHTGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYA 120 VKALTEQAGKFWHTGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYA Sbjct: 61 VKALTEQAGKFWHTGNGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYA 120 Query: 121 HDRFGSEKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALI 180 HDRFGSEKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALI Sbjct: 121 HDRFGSEKSGIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALI 180 Query: 181 DDNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMH 240 DDNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMH Sbjct: 181 DDNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMH 240 Query: 241 YGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATIN 300 YGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATIN Sbjct: 241 YGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATIN 300 Query: 301 TREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAE 360 TREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAE Sbjct: 301 TREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAE 360 Query: 361 EGLMILIAGANVVRFAPALIISEDEVNSGLDRFELACKRFLAGVSS 406 EGLMILIAGANVVRFAPALIISEDEVNSGLDRFELACKRFLAGVSS Sbjct: 361 EGLMILIAGANVVRFAPALIISEDEVNSGLDRFELACKRFLAGVSS 406 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: 708 Number of extensions: 19 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 BWI76_RS11670 BWI76_RS11670 (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.aa/TIGR03246.hmm # target sequence database: /tmp/gapView.1012.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-228 743.3 0.2 3.7e-228 743.1 0.2 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS11670 BWI76_RS11670 aspartate aminotra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS11670 BWI76_RS11670 aspartate aminotransferase family protein # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 743.1 0.2 3.7e-228 3.7e-228 1 396 [. 5 400 .. 5 401 .. 1.00 Alignments for each domain: == domain 1 score: 743.1 bits; conditional E-value: 3.7e-228 TIGR03246 1 veresfdevmvpvyapakfipvrgeGsrvwdqegkeyidfaGGiavnalGhahpelvealkeqaeklwhlg 71 ++r++fde+m+pvyapa+fipvrgeGsr+wdq+gkeyidfaGGiavnalGhahp lv+al+eqa k+wh+g lcl|FitnessBrowser__Koxy:BWI76_RS11670 5 ITRSNFDEWMMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTG 75 79********************************************************************* PP TIGR03246 72 ngytnepvlrlakklvdatfadkvffcnsGaeaneaalklarkvaldkygaekseivafknsfhGrtlftv 142 ngytnepvlrlak+l+datfad+vffcnsGaeaneaalklark+a+d++g+eks ivafkn+fhGrtlftv lcl|FitnessBrowser__Koxy:BWI76_RS11670 76 NGYTNEPVLRLAKQLIDATFADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGRTLFTV 146 *********************************************************************** PP TIGR03246 143 svGGqakysedfaplpegikhaayndlealkalisdktcavivepiqGegGvvpadkaflkglrelcdrhn 213 s+GGq++ys+dfaplp +i+ha+yndl+++kali+d+tcavivep+qGegGvvpad +fl+glrelcd+hn lcl|FitnessBrowser__Koxy:BWI76_RS11670 147 SAGGQPAYSQDFAPLPPQIQHAIYNDLDSAKALIDDNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHN 217 *********************************************************************** PP TIGR03246 214 allifdevqtGvGrtGelyaymeyGvtpdiltsakalGgGfpiGalltteelakvlkvGthGttyGGnpla 284 allifdevqtGvGrtGelyaym+yGvtpd+l++akalGgGfpiGall++e++a+v++vGthGttyGGnpla lcl|FitnessBrowser__Koxy:BWI76_RS11670 218 ALLIFDEVQTGVGRTGELYAYMHYGVTPDLLSTAKALGGGFPIGALLASERCASVMTVGTHGTTYGGNPLA 288 *********************************************************************** PP TIGR03246 285 cavaekvldlvntaelleGvkqrhelfvdelekinarykvfseirGkGlliGavlteeyaGkakdlvnaaa 355 cava++v+ ++nt e+l+Gvkqrh++f ++l++inary +f+eirG GlliG+vl++eyaGkak + n+aa lcl|FitnessBrowser__Koxy:BWI76_RS11670 289 CAVAGEVFATINTREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAA 359 *********************************************************************** PP TIGR03246 356 eeGvlvliaGpdvvrfapslvieeeeikeGlarlekavekl 396 eeG+++liaG++vvrfap+l+i+e+e++ Gl+r+e a++++ lcl|FitnessBrowser__Koxy:BWI76_RS11670 360 EEGLMILIAGANVVRFAPALIISEDEVNSGLDRFELACKRF 400 **************************************987 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.14 // [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