Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_101445362.1 BD749_RS13990 aspartate aminotransferase family protein
Query= reanno::Koxy:BWI76_RS11670 (406 letters) >NCBI__GCF_002846395.1:WP_101445362.1 Length = 396 Score = 204 bits (519), Expect = 4e-57 Identities = 126/373 (33%), Positives = 203/373 (54%), Gaps = 29/373 (7%) Query: 27 RGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQAGKFWH--TGNGYTNEPVL 84 + EG ++ G YID GI V+ +GH HP++++A+ +Q ++ H + P Sbjct: 26 KAEGIYMYGSDGHRYIDLISGIGVSNVGHRHPKVLRAIHDQLDRYMHLMVYGEFVQGPQA 85 Query: 85 RLAKQLIDAT--FADRVFFCNSGAEANEAALKLARKYAHDRFGSEKSGIVAFKNAFHGRT 142 +LA+ L + V+ NSG EA E A+KLA++Y + ++G V +NA+HG T Sbjct: 86 QLAQALCSTLPPRLNNVYLLNSGTEAVEGAMKLAKRY------TGRTGFVTCRNAYHGST 139 Query: 143 LFTVSAGGQPAYSQDFAPLPPQIQ---HAIYNDLDSAKALIDDNTCAVIVEPMQGEGGVV 199 +S G + F PL P ++ H DL I ++T A+I+E +QGE G+ Sbjct: 140 QGALSVNGSEGFKNAFRPLLPDVRVINHGAIPDLQQ----ITEHTAAIIIEAVQGEAGLR 195 Query: 200 PADADFLRGLRELCDAHNALLIFDEVQTGVGRTGELYAYMHYGVTPDLLSTAKALGGGFP 259 +A +++ LR+ C ALLI DE+QTG GRTG +A+ +G+ PD+L AK +GGG P Sbjct: 196 VPEASYMQALRDRCTEVGALLILDEIQTGFGRTGTFWAFEQFGIEPDILLCAKGMGGGMP 255 Query: 260 IGALLASERCASVM---TVGTHGTTYGGNPLACAVAGEVFATINTREVLNGVKQRHQWFC 316 IGA +A + +V + H TT+GG+P++CA + TI +L GV+++ F Sbjct: 256 IGAFIAPQEIMAVFKNDPILGHLTTFGGHPVSCAASLATLQTIQEENLLAGVEEKANLFR 315 Query: 317 ERLNAINARYGLFKEIRGLGLLIGCVLKDEYAGKAKAISNQAAEEGLMI--LIAGANVVR 374 E L ++ R K IR GL++ + E KA+ +QA G++ + N +R Sbjct: 316 ELL--VHPR---IKGIRNKGLMMAA--EFESFEVLKAVIDQAIVNGVLTDWFLFCDNSMR 368 Query: 375 FAPALIISEDEVN 387 AP LII+E++++ Sbjct: 369 IAPPLIITEEQIH 381 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: 414 Number of extensions: 28 Number of successful extensions: 6 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: 396 Length adjustment: 31 Effective length of query: 375 Effective length of database: 365 Effective search space: 136875 Effective search space used: 136875 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 Jul 26 2024. The underlying query database was built on Jul 25 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