Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate Synpcc7942_0943 Synpcc7942_0943 acetylornithine aminotransferase
Query= reanno::WCS417:GFF4238 (406 letters) >FitnessBrowser__SynE:Synpcc7942_0943 Length = 422 Score = 323 bits (829), Expect = 4e-93 Identities = 182/405 (44%), Positives = 239/405 (59%), Gaps = 8/405 (1%) Query: 6 APVQRADFDQVMVPNYAPAAFIPVRGEGSRVWDQAGRELIDFAGGIAVNVLGHAHPALVG 65 +P FD ++ Y RGEG RVWD GR +DF GIA LGHAHP LV Sbjct: 16 SPFSTDAFDACVMQTYGRFPLALERGEGCRVWDTQGRSYLDFVAGIATCTLGHAHPELVD 75 Query: 66 ALTEQAHKLWHVSNVFTNEPALRLAHKLIDATFAERVFFCNSGAEANEAAFKLARRVAFD 125 A+++Q KL HVSN++ +LA L + A+RVFFCNSGAEANEAA KLAR+ Sbjct: 76 AISDQIRKLHHVSNLYYIPEQGQLAAWLTANSCADRVFFCNSGAEANEAAIKLARKHGNT 135 Query: 126 RFGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLDALKA---- 181 +E I+ A SFHGRTL V GQ KY GF P + G +VPYNDL AL+A Sbjct: 136 VLEAENPIILTAQASFHGRTLAAVTATGQPKYHKGFQPLVQGFRYVPYNDLAALEATLAE 195 Query: 182 --AVSDKTCAVVLEPIQGEGGVLPAELAYLQGARDLCDANNALLVFDEVQTGMGRSGHLF 239 A + A++LEP+QGEGGV P + AY Q R LCD LL+ DEVQ GMGRSG L+ Sbjct: 196 LDAAGETVAAILLEPLQGEGGVNPGDRAYFQAVRQLCDQRRMLLILDEVQVGMGRSGQLW 255 Query: 240 AYQHYGVTPDILTSAKSLGGGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVI 299 Y++ G+ PD T AK LGGG PI A+L +A L G H +T+GGNPLAC A+ Sbjct: 256 GYENLGIEPDAFTVAKGLGGGVPIGALL-VKASCNILQAGEHASTFGGNPLACRAGLAIA 314 Query: 300 DVINTPEVLAGVNAKHDLFKARLEQIGKQY-GIFTEVRGMGLLLGCVLSDAFKGKAKDVF 358 V+ ++LA V A+ + +A L+++ +Y + VRG GL+ G VL + + Sbjct: 315 QVMERDQLLANVQARGEQLRAGLQELVDRYPNLLAGVRGWGLINGLVLRNDPNVTPIALV 374 Query: 359 NAAEKENLMILQAGPDVVRFAPSLVVEDADIKEGLDRFERAVKAL 403 AA ++ L+++ AG +VVRF P L+V A+I E L ERA+ A+ Sbjct: 375 KAAIEQGLLLVPAGAEVVRFVPPLIVSAAEIDEALAMTERALLAI 419 Lambda K H 0.320 0.137 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: 443 Number of extensions: 20 Number of successful extensions: 4 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: 422 Length adjustment: 31 Effective length of query: 375 Effective length of database: 391 Effective search space: 146625 Effective search space used: 146625 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 Aug 03 2021. The underlying query database was built on Aug 03 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