Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_012282524.1 HM1_RS06545 acetylornithine transaminase
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >NCBI__GCF_000019165.1:WP_012282524.1 Length = 432 Score = 349 bits (896), Expect = e-101 Identities = 181/378 (47%), Positives = 246/378 (65%), Gaps = 4/378 (1%) Query: 29 VRGAGSRVWDQSGRELIDFAGGIAVNVLGHAHPALVAALTEQANKLWHVSNVFTNEPALR 88 V+G G+R+WD GRE +DF G+AVN LGH HP +V AL +QA L HVSN++ EP ++ Sbjct: 26 VKGQGARLWDADGREYLDFLAGLAVNSLGHCHPKVVDALQQQAATLLHVSNLYWIEPQVQ 85 Query: 89 LAHKLVDATFAERVFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFHGRTLFT 148 LA LV+ +FA++VFFCNSGAEANE A KLAR+ A +G++KYEI+ SFHGRTL T Sbjct: 86 LAQVLVENSFADKVFFCNSGAEANEGAIKLARKYAKKTWGSDKYEIITMEKSFHGRTLAT 145 Query: 149 VNVGGQSKYSDGFGPKITGITHVPYNDLAALKAAVSDKTCAVVLEPIQGEGGVLPAELSY 208 V Q KY + P G +VP+ DL AL+ A+S TCA+++EP+QGEGGV AE S+ Sbjct: 146 VTATAQPKYQKDYEPLPQGFRYVPFGDLKALERAISPHTCAILVEPVQGEGGVNLAEPSF 205 Query: 209 LQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPDILTSAKSLGGGFPIAAMLT 268 QG +L A+ LL+FDEVQ G+GR+GKLFA++HYGVTP I+T AK+L GG P+ A+L Sbjct: 206 WQGLAKLAAANKLLLIFDEVQCGLGRTGKLFAHEHYGVTPHIMTLAKALAGGAPMGALLA 265 Query: 269 TEDLAKHLVVGTHGTTYGGNPLACAVAEAVIDVINTPEVLNGVNAKHDKFKTRLEQIGEK 328 T+D+A G H +T+GGNPL A A AV+DV+ +++ F L ++ EK Sbjct: 266 TDDVANAFQPGDHASTFGGNPLVAAAAVAVMDVLLNDGLMDNCREMAAYFMGHLRRLQEK 325 Query: 329 YGLFTEVRGLGLLLGCVLSDAWKGKAKDIFNAAEREGLMILQAGPDVIRFAPSLVVEDAD 388 Y TEVRGLGL++ C L + A + N E+ GL+I +V+RF P L++ AD Sbjct: 326 YPFITEVRGLGLMVACELD---RPGADIVANCLEK-GLIINCTAGNVLRFLPPLIINKAD 381 Query: 389 IDAGLDRFERAAAKLTQA 406 +D + E A + A Sbjct: 382 VDEAVAVLEEVLASVVAA 399 Lambda K H 0.320 0.136 0.400 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: 441 Number of extensions: 18 Number of successful extensions: 2 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: 432 Length adjustment: 32 Effective length of query: 374 Effective length of database: 400 Effective search space: 149600 Effective search space used: 149600 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