Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_025763135.1 X939_RS0110060 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >NCBI__GCF_000566685.1:WP_025763135.1 Length = 384 Score = 219 bits (559), Expect = 8e-62 Identities = 146/397 (36%), Positives = 211/397 (53%), Gaps = 34/397 (8%) Query: 14 MMPVYAPAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWH 73 + VY PV+ +GS LWDQ G EY+D GG AV ++GH HP V LTEQ K Sbjct: 4 LFEVYPLYDIEPVKAQGSYLWDQNGIEYLDMYGGHAVISVGHCHPDYVARLTEQLSKISF 63 Query: 74 TGNGYTNEPVLRLAKQLIDAT-FAD-RVFFCNSGAEANEAALKLARKYAHDRFGSEKSGI 131 N LA +L + + D ++F CNSGAEANE ALKLA F + + + Sbjct: 64 YSNSVQIPQQEELATKLGTLSGYPDYKLFLCNSGAEANENALKLAS------FHTGRKKV 117 Query: 132 VAFKNAFHGRTLFTVSAGGQPA------YSQDFAPLPPQIQHAIYNDLDSAKALIDDNTC 185 VAF AFHGRT V+A P+ Y++ + LP +ND+++ +A I + Sbjct: 118 VAFTKAFHGRTAGAVAATDNPSIVAPVNYNEHVSFLP-------FNDIEALQAGITEEVA 170 Query: 186 AVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTP 245 AVIVE +QG GG+ +FL+ LR+ CD A LI D VQ G GRTG+ +++ G+ P Sbjct: 171 AVIVEGIQGVGGIQVCSDEFLQALRKRCDETGAALILDSVQCGYGRTGKFFSHQFSGIHP 230 Query: 246 DLLSTAKALGGGFPI-GALLASERCASVMTVGTHGTTYGGNPLACAVAGEVFATINTREV 304 D+++ AK +G GFPI G L+A + AS G GTT+GGN LACA V + ++ Sbjct: 231 DMMTMAKGMGNGFPIAGVLIAPQFKAS---FGLLGTTFGGNHLACAAGIAVLDIMKDEQL 287 Query: 305 LNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAA-EEGL 363 L+ + + + + G +K++RG GL+IG E+ K + N+ E + Sbjct: 288 LDNATKIGAYLFHEIEEL----GGYKDLRGRGLMIGI----EFDFPVKELRNKLLFEHHI 339 Query: 364 MILIAGANVVRFAPALIISEDEVNSGLDRFELACKRF 400 +AGA +R P+L IS+ E + L+ + K F Sbjct: 340 FTGVAGAYTLRLLPSLAISQKEADQFLEAYRSCLKTF 376 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: 393 Number of extensions: 20 Number of successful extensions: 7 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: 384 Length adjustment: 31 Effective length of query: 375 Effective length of database: 353 Effective search space: 132375 Effective search space used: 132375 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)
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