Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate 5211158 Shew_3574 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::Q9K9B2 (515 letters) >FitnessBrowser__PV4:5211158 Length = 506 Score = 223 bits (567), Expect = 2e-62 Identities = 151/444 (34%), Positives = 231/444 (52%), Gaps = 27/444 (6%) Query: 62 QLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEFSAWLVH 121 Q+ V+++++ E A+ +A A W + ER+N+L+K A + + + Sbjct: 45 QVFCQVARSDERDIELALDAAHAAKDAWGKTSVTERSNLLLKIADRVEQNLEFLAVAETW 104 Query: 122 EAGKPWKEA-DADTAEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISP 180 E GK +E +AD +D Y+A I G + +F P+GV I P Sbjct: 105 ENGKAVRETLNADLPLFVDHFRYFAG-CIRAQEGSAADIDNNTVSYHFPEPLGVVGQIIP 163 Query: 181 WNFALAIMVGTAVAP-IVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGA 239 WNF L +M +AP + GN +VLKPA TPV VE+++D LP GV+N V G G Sbjct: 164 WNFPL-LMAAWKIAPALAAGNCIVLKPAEQTPVSILVMVELIQDL-LPAGVLNIVNGFGT 221 Query: 240 EVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKDT------V 293 E G L + + + FTGS +G + + AA L VE+GGK V Sbjct: 222 EAGQALAVSKRIAKLAFTGSTQIGHHILKCAA------ESLIPSTVELGGKSPNIYFADV 275 Query: 294 VVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPT 353 + D LD A E +L++ F G+ C+ SR +I + +YD+ ++K +A AK + G+P Sbjct: 276 MEQEDEYLDKAVEGMLLAFFN-QGEVCTCPSRVLIAESIYDKFIDKVIARAKTIKQGNPL 334 Query: 354 NRDNYMGPVIDEKAFEKIMSYIEIGKKEG-RLMTGG-----EGDSSTGFFIQPTIIADLD 407 + D +G ++ F+KI+SY+EIG+ EG ++ GG GD S+GF+I+PTI+ + Sbjct: 335 DTDTQVGAQASQEQFDKILSYLEIGRNEGAEVLIGGTSCQLSGDQSSGFYIEPTILKGHN 394 Query: 408 PEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGN 467 + + QEEIFGPV++ + D AL IAN+TEYGL V TR+ ++ R G Sbjct: 395 -KMRVFQEEIFGPVISVTTFKDEAEALAIANDTEYGLGAGVWTRDMNRAQRMGRGIQAGR 453 Query: 468 LYFNRNCTGAIVGYHPFGGFKMSG 491 ++ NC A + FGG+K SG Sbjct: 454 VWI--NCYHAYPAHAAFGGYKKSG 475 Lambda K H 0.316 0.134 0.388 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: 605 Number of extensions: 31 Number of successful extensions: 7 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: 515 Length of database: 506 Length adjustment: 35 Effective length of query: 480 Effective length of database: 471 Effective search space: 226080 Effective search space used: 226080 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