Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_066608605.1 V473_RS18720 diaminobutyrate--2-oxoglutarate transaminase
Query= reanno::pseudo1_N1B4:Pf1N1B4_3440 (406 letters) >NCBI__GCF_001046645.1:WP_066608605.1 Length = 436 Score = 140 bits (352), Expect = 9e-38 Identities = 119/393 (30%), Positives = 189/393 (48%), Gaps = 42/393 (10%) Query: 36 VW--DQSGRELIDFAGGIAVNVLGHAHPALVAALTEQA--NKLWHVSNVFTNEPALRLAH 91 VW D G +DF G + GH HP L AL + + + H ++ T+ A LA Sbjct: 43 VWMHDNQGGRYLDFLSGCSTLNYGHNHPVLKNALVDYIVNDGITHGLDLHTDAKADFLA- 101 Query: 92 KLVDATFAER------VFFCNSGAEANEAAFKLARRVAHDRFGTEKYEIVAALNSFHGRT 145 L D R +F +G A EAA KLAR++ T + ++A N FHG T Sbjct: 102 ALEDVILTPRDLDYRAMFTGPTGTNAVEAAIKLARKI------TGRELVIAFTNGFHGMT 155 Query: 146 LFTVNVGGQSKYSDGFGPKITGITHVPYN-------DLAA-LKAAVSDKT------CAVV 191 L + G + G G + ++H PY+ D A L+ +SD + A++ Sbjct: 156 LGALACTGNAAKRGGAGVPLNHVSHEPYDGYHGPGVDTAEQLERRLSDPSSGLDAPAAIL 215 Query: 192 LEPIQGEGGVLPAELSYLQGARELCDAHNALLVFDEVQTGMGRSGKLFAYQHYGVTPDIL 251 +E +QGEGG+ A +L+ ++ H AL++ D++Q G GR+G F+++ G TPDI+ Sbjct: 216 VETVQGEGGLNAASPRWLRQIADIAKRHGALMIIDDIQAGCGRTGNFFSFEGMGFTPDIV 275 Query: 252 TSAKSLGG-GFPIAAMLTTEDLAKHLVVGTHGTTYGGNPLACAVAEAVI-DVINTPEVLN 309 T AKSL G G P A L +L G H T+ GN A A A + + Sbjct: 276 TMAKSLSGMGLPFALTLFRPEL-DQWSPGEHNGTFRGNNHAFVTATATLRHFWSDGNFQQ 334 Query: 310 GVNAKHDKFKTRLEQIGEKYGLFTEVRGLGLLLGCVLSDAWKGK-AKDIFNAAEREGLMI 368 + + + RL + ++GL +RG G++ G D G+ A+ I A +GL+I Sbjct: 335 DIARRGALLERRLAAMATEHGL--SIRGRGMMRGI---DVGSGEIAQTITAACFAQGLII 389 Query: 369 LQAG--PDVIRFAPSLVVEDADIDAGLDRFERA 399 +G ++++ LV++D+ + AGLD E++ Sbjct: 390 ETSGAHDEIVKVLAPLVIDDSVLSAGLDILEQS 422 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: 446 Number of extensions: 29 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: 436 Length adjustment: 32 Effective length of query: 374 Effective length of database: 404 Effective search space: 151096 Effective search space used: 151096 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 Sep 24 2021. The underlying query database was built on Sep 17 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