Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_012503231.1 CPAR_RS10185 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >NCBI__GCF_000020505.1:WP_012503231.1 Length = 424 Score = 143 bits (361), Expect = 8e-39 Identities = 131/407 (32%), Positives = 196/407 (48%), Gaps = 58/407 (14%) Query: 20 PAAFIPVRG-EGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWHTG-NG 77 P PV+ G + + G++ ID G+ HP L +A TEQ + H G Sbjct: 20 PLPVYPVKSASGVMIELEDGRQLIDGMSSWWAAIHGYNHPVLNRAATEQLERMSHVMFGG 79 Query: 78 YTNEPVLRLAKQLIDATF--ADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFK 135 T+EP + L K LI D VFFC+SG+ + E A+K+A +Y +K ++ + Sbjct: 80 LTHEPAIELGKILISLLPDPLDSVFFCDSGSVSVEVAIKMALQYWRAAGKPDKKRLLTVR 139 Query: 136 NAFHGRTLFTVSA-----GGQPAYS-----QDFAPLP------PQIQHAIYNDLDSAKAL 179 + +HG T +S G +S Q F P P + AI + +AL Sbjct: 140 SGYHGDTFMAMSVCDPVTGMHSLFSGAVPEQLFVESPSCGFGEPWREEAIE---EMRQAL 196 Query: 180 ID--DNTCAVIVEPM-QGEGGVVPADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELY 236 D D AVI+EP+ QG GG+ +L+ LRELC H LLIFDE+ TG GRTG+L+ Sbjct: 197 EDHADTIAAVIIEPIVQGAGGMRFYSPVYLQRLRELCTEHGVLLIFDEIATGFGRTGKLF 256 Query: 237 AYMHYGVTPDLLSTAKALGGGF-PIGALLASERCASVMTVG-----THGTTYGGNPLACA 290 A GVTPD++ KAL GG+ + A +A+ A ++ G HG T+ NPLACA Sbjct: 257 AMERAGVTPDIVCLGKALTGGYMTLAATIATGHVADTISGGDPGLFMHGPTFMANPLACA 316 Query: 291 VA---------GEVFATIN--TREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLLI 339 VA G+ AT+ R++ G+ C +L+A+ +++R LG + Sbjct: 317 VAVASLRLLLSGDWRATVQRIERQLAEGLAP-----CVKLSAV-------RDVRVLGAI- 363 Query: 340 GCVLKDEYAGKAKAISNQAAEEGLMILIAGANVVRFAPALIISEDEV 386 V++ + +I + E G+ + G +V P IISE E+ Sbjct: 364 -GVVELYHPVDMASIQKRFVEYGVWVRPFG-RLVYLMPPFIISEAEL 408 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: 386 Number of extensions: 15 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: 424 Length adjustment: 31 Effective length of query: 375 Effective length of database: 393 Effective search space: 147375 Effective search space used: 147375 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 Apr 10 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