Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate SM_b21186 SM_b21186 4-aminobutyrate aminotransferase
Query= SwissProt::P18335 (406 letters) >FitnessBrowser__Smeli:SM_b21186 Length = 422 Score = 227 bits (579), Expect = 4e-64 Identities = 139/406 (34%), Positives = 204/406 (50%), Gaps = 39/406 (9%) Query: 30 KGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHISN-VFTNEPALR 88 + + + IWD++G Y+DFA GIAV GH HP ++ A+K Q + H + V E + Sbjct: 26 RAENAEIWDKEGNRYIDFAAGIAVVNTGHRHPKVIAAVKAQLDRFTHTCHQVVPYENYVH 85 Query: 89 LGRKL---IEATFAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRS 145 L +L + FA++ +F+ +G EA E A K+AR + + ++AF FHGR+ Sbjct: 86 LAERLNAIVPGDFAKKTIFVTTGAEAVENAVKIARA------ATGRQAVVAFGGGFHGRT 139 Query: 146 LFTVSVGGQP-KYSDGFGPKPADIIHVPFN-DLHAVKA--------------VMDDHTCA 189 +++ G+ Y GFG PAD+ H PF +LH V V A Sbjct: 140 FMGMALTGKVVPYKVGFGAMPADVFHAPFPIELHGVTVEQSLSALKKLFAADVDPARVAA 199 Query: 190 VVVEPIQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTPD 249 +++EP+QGEGG F++ LRE+CDQH LL+ DEVQ G RTG LFA H+GV PD Sbjct: 200 IIIEPVQGEGGFYPVPTAFMKALREVCDQHGILLIADEVQTGFARTGKLFAMEHHGVAPD 259 Query: 250 ILTSAKALGGGFPISAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEVLE 309 + T AK+L GGFP++A+ AEI A PG G TYGGNPL A A A D+I + E Sbjct: 260 LTTMAKSLAGGFPLAAVTGRAEIMDAPGPGGLGGTYGGNPLGIAAAHAVLDVIAEENLCE 319 Query: 310 GIQAKRQRFVDHLQKIDQQYDVFSDIRGMGLLIGAEL--------KPQYKGRARDFLYAG 361 R L I ++ DIRG G + E ++ + R Sbjct: 320 RANQLGNRLKQRLAAIREKAPEIVDIRGPGFMNAVEFNDVRTNLPSAEFANKVR---LLA 376 Query: 362 AEAGVMVLNAG--PDVMRFAPSLVVEDADIDEGMQRFAHAVAKVVG 405 E G+++L G +V+RF + ++D E + ++ + G Sbjct: 377 LEKGLILLTCGVHGNVIRFLAPITIQDEVFAEALDTIEASILEARG 422 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: 473 Number of extensions: 22 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: 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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