Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate WP_011840643.1 RSPH17029_RS04315 4-aminobutyrate--2-oxoglutarate transaminase
Query= SwissProt::P18335 (406 letters) >NCBI__GCF_000015985.1:WP_011840643.1 Length = 425 Score = 228 bits (582), Expect = 2e-64 Identities = 141/395 (35%), Positives = 204/395 (51%), Gaps = 33/395 (8%) Query: 34 SRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHISN-VFTNEPALRLGRK 92 + IWD +G+ Y+DFA GIAV GHCHP ++ A+ Q H + V E +RL + Sbjct: 32 AEIWDIEGRRYIDFAAGIAVVNTGHCHPKVMAAVAEQMGRFTHTCHQVLPYENYIRLAER 91 Query: 93 LIEAT---FAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLFTV 149 L A FA++ VF+ +G E+ E A K+AR + ++ ++AF FHGR+ T+ Sbjct: 92 LNAAAPGDFAKKTVFVTTGAESVENAIKIARIHTG------RSAVVAFGGGFHGRTFMTM 145 Query: 150 SVGGQPK-YSDGFGPKPADIIHVPFND-LHAV-------------KAVMDD-HTCAVVVE 193 S+ G+ + Y GFG ++ HVPF LH + KA +D A++ E Sbjct: 146 SLTGKVEPYKKGFGTMMPEVYHVPFPQALHGISTEEAMAALARLFKADLDPGRVAAIIFE 205 Query: 194 PIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTS 253 P+QGEGG A P+ ++ +R+LCD H +++ DEVQ G RTG LFA Y V PD++T Sbjct: 206 PVQGEGGFYPAPPDLVRAIRQLCDAHGIVMIADEVQTGFARTGTLFAMHGYDVAPDLVTM 265 Query: 254 AKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEVLEGIQA 313 AK LGGG PI+A+ AEI A HPG G TYGGNPL A A A D+I + Sbjct: 266 AKGLGGGLPIAAVTGRAEIMDAAHPGGLGGTYGGNPLGIAAAHAVLDVIEEENLCARATE 325 Query: 314 KRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAEL-----KPQYKGRARDFLYAGAEAGVMV 368 R L +I +DIRG G ++GAE K G + G+++ Sbjct: 326 LGSRLKQKLAEIRATAPEIADIRGPGFMVGAEFADPGSKAPDAGFTNRVREEALKRGLIL 385 Query: 369 LNAG--PDVMRFAPSLVVEDADIDEGMQRFAHAVA 401 L G +V+RF + + + E ++ +VA Sbjct: 386 LTCGVHGNVIRFLAPITIPEPHFAEALEILEASVA 420 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: 497 Number of extensions: 23 Number of successful extensions: 5 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: 425 Length adjustment: 31 Effective length of query: 375 Effective length of database: 394 Effective search space: 147750 Effective search space used: 147750 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 31 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