Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate H281DRAFT_02680 H281DRAFT_02680 succinate semialdehyde dehydrogenase
Query= reanno::MR1:199807 (487 letters) >FitnessBrowser__Burk376:H281DRAFT_02680 Length = 492 Score = 201 bits (511), Expect = 5e-56 Identities = 158/475 (33%), Positives = 232/475 (48%), Gaps = 36/475 (7%) Query: 4 FIKGQW-HTGKGHDVASSNPANGEIIWRGQTATAEQVNAAVDAAREAQFDWFILGFDARL 62 +I GQW A +PA GE I T + A++A AQ W L R Sbjct: 23 YIDGQWCGADDARTFAVDDPATGEKIADVPLMTGAETRRAIEAGEHAQRGWRKLTAAQRS 82 Query: 63 KIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSASAYN------KRT 116 I++ + + + AN +LA ++ E GKP +A G+IG +AS KR Sbjct: 83 TILKRWHALMIANTDDLAIIMSAEQGKP-------LAEAKGEIGYAASFIEWFAEQAKRV 135 Query: 117 GTETNDTPAG--RAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVVFKPSELTP 174 + +PA R ++ +P GV A P+NFP + + PAL AG +++ KP+E TP Sbjct: 136 DGDVLASPAADKRMLVTKEPIGVCAAITPWNFPAAMITRKVAPALAAGCAMILKPAEATP 195 Query: 175 KVAELMVTLWEKSGLPAGVLNLVQGEV-DTGKALASHPQLDGLFFTGSSRTGHLLHQQYA 233 A + L ++G+PAGV ++V G+ G + S+P + L FTGS+ G +L Q A Sbjct: 196 LSALALAELAHRAGVPAGVFSVVVGDPRSIGAEMTSNPIVRKLSFTGSTPVGRMLMSQCA 255 Query: 234 GHPGKILALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDA 293 K L+LE+GGN P I+ AD+ AAV L S Y ++GQ C C R+YV+ G DA Sbjct: 256 PTVKK-LSLELGGNAPFIVFDDADLDAAVEGALASKYRNAGQTCVCTNRVYVQDGVY-DA 313 Query: 294 LVAKLVEAVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQANLLSLGGVPLVELMHLQA 353 K AV +IKVG + G +I+EAA + + A A+ ++ G L A Sbjct: 314 FAEKFAAAVGRIKVGN-GFESGVTQGPLINEAAVEKVEAHIADAVAHGARVLTGGKRHAA 372 Query: 354 GTGLVSPGLI-DVTAVSELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSA------- 405 G P ++ DVTA EE FGP+ L R+++ +AI AN T +GL+A Sbjct: 373 GKLFFEPTVVGDVTARMRFATEETFGPVAPLFRFTNEREAIAAANATEFGLAAYFYSRDI 432 Query: 406 GILADSREDYEYFLARIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAAD 460 G + E EY + I G++ ++ APFGGV SG R + Y + Sbjct: 433 GRIWRVAEALEYGMVGINTGLI--------SNEVAPFGGVKQSGLGREGSKYGIE 479 Lambda K H 0.316 0.133 0.391 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: 587 Number of extensions: 35 Number of successful extensions: 6 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: 487 Length of database: 492 Length adjustment: 34 Effective length of query: 453 Effective length of database: 458 Effective search space: 207474 Effective search space used: 207474 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 (21.6 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