Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate RR42_RS26240 RR42_RS26240 4-aminobutyrate aminotransferase
Query= SwissProt::P18335 (406 letters) >FitnessBrowser__Cup4G11:RR42_RS26240 Length = 420 Score = 247 bits (630), Expect = 5e-70 Identities = 149/397 (37%), Positives = 214/397 (53%), Gaps = 38/397 (9%) Query: 26 FIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHIS-NVFTNE 84 F + + S +WD +G Y+DFA GIAV GH HP LV A++ Q E H + + Sbjct: 24 FYAERAENSELWDVEGNRYIDFAAGIAVLNTGHRHPRLVQAMQAQMERFTHTAYQIVPYA 83 Query: 85 PALRLGRKL---IEATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAF 141 + L K+ FA++ F +G EA E A K+AR + + +IAF F Sbjct: 84 SYIELAEKINARAPGAFAKKTAFFTTGAEAVENAIKIARA------ATGRPGVIAFSGGF 137 Query: 142 HGRSLFTVSVGGQP-KYSDGFGPKPADIIHVPF-------------NDLHAV-KAVMDD- 185 HGR++ +++ G+ Y GFGP P D+ H P+ N LH + KA +D Sbjct: 138 HGRTMMGMALTGKVVPYKVGFGPFPGDVFHAPYPYGLHGVSVQDSINALHQLFKADVDPK 197 Query: 186 HTCAVVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYG 245 A++ EP+QGEGG A EF++ LR +CD+H LLV DEVQ G GRTG LFA HY Sbjct: 198 RVAAIIFEPVQGEGGFNVAPAEFVRALRAICDEHGILLVADEVQTGFGRTGKLFAMEHYD 257 Query: 246 VTPDILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTP 305 VTPD+ T AK+L GG P+SA+ AEI A PG G TY GNPLA A A A D++ + Sbjct: 258 VTPDLTTMAKSLAGGMPLSAVCGRAEIMDAPAPGGLGGTYAGNPLAVASALAVLDVLESE 317 Query: 306 EVLEGIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAELK-------PQYKGRARDFL 358 +++E A QR D L + + ++RG+G +I E + P++ + +D Sbjct: 318 KLIERGAALGQRLQDKLDGLKSRVPEIGEVRGVGAMIAVEFRKADGRPDPEFTRQVQD-- 375 Query: 359 YAGAEAGVMVLNAG--PDVMRFAPSLVVEDADIDEGM 393 E G+++L+ G +V+RF L + DA +DEG+ Sbjct: 376 -RALERGLLLLSCGVYGNVVRFLFPLTIPDAVMDEGL 411 Lambda K H 0.322 0.138 0.415 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: 474 Number of extensions: 29 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: 420 Length adjustment: 31 Effective length of query: 375 Effective length of database: 389 Effective search space: 145875 Effective search space used: 145875 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 (21.9 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