Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate 6939342 Sama_3435 aldehyde dehydrogenase (RefSeq)
Query= reanno::WCS417:GFF827 (481 letters) >FitnessBrowser__SB2B:6939342 Length = 506 Score = 276 bits (706), Expect = 1e-78 Identities = 172/466 (36%), Positives = 246/466 (52%), Gaps = 18/466 (3%) Query: 6 RFDNYINGQWV--AGADYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPAWSTSG 63 R+DN+I G+WV G +Y N++P + V + A++D + A+DAA AA +W + Sbjct: 18 RYDNFIGGKWVPPVGGEYFDNVSPVD-GKVFCQAARSDYRDIELALDAAHAAKDSWGKTS 76 Query: 64 IQARHDALDKVGSEILARREELGTLLAREEGKTLPEAIG-EVTRAGNIFKFFAGECLRLS 122 + R + L K+ + E L + E GK + E + ++ + F++FAG C+R Sbjct: 77 VTERSNLLLKIADRVEQHLERLAVVETWENGKAVRETLNADLPLFVDHFRYFAG-CIRAQ 135 Query: 123 GDYVPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPG 182 + E LGVVG I PWNFP+ + AWKIAPALA GNCVV+KPAE P Sbjct: 136 EGSAADLDANTVSYHLPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQTPA 195 Query: 183 CAWALAEIISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVSCVS 242 L E I P GV N+V G G G L S ++ ++FTGS VG I Sbjct: 196 SIMVLLETIEDL-LPPGVLNVVNGFGAEAGAALATSKRIAKLAFTGSTEVGNHILKCAAE 254 Query: 243 RQAKVQLEMGGKNPQIIL------DDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAGI 296 +E+GGK+P I +D L +A+E + AF++ G+ CT SR++V I Sbjct: 255 NLIPSTVELGGKSPNIYFADVMNHEDNYLDKAIE-GMLLAFFNQGEVCTCPSRVLVQESI 313 Query: 297 HDQFVAAMAERMKSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGLV 356 +D F+ + R K+I+ G L + T +G S+ Q D+ L Y+DIG++EGA+++ GG Sbjct: 314 YDAFIEKVIARAKTIRQGSPLDTDTQVGAQASREQYDKILGYLDIGRAEGAKVLMGGEFK 373 Query: 357 TCD---TEGYYLAPTLFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSA 413 D GYY+ PT+ MR+ +EEIFGPV +V D ALA+ANDT++GL A Sbjct: 374 LQDGPEKGGYYIQPTIL-KGHNKMRVFQEEIFGPVVSVTTFKDEAEALAIANDTQYGLGA 432 Query: 414 GIATTSLKYANHFKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYG 459 G+ T + A R QAG V +N A H FGG K S G Sbjct: 433 GVWTRDMNLAQRMGRGIQAGRVWINCYHA-YPAHAAFGGYKKSGIG 477 Lambda K H 0.318 0.134 0.390 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: 532 Number of extensions: 24 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: 481 Length of database: 506 Length adjustment: 34 Effective length of query: 447 Effective length of database: 472 Effective search space: 210984 Effective search space used: 210984 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 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