Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate PP_0708 PP_0708 putative Betaine-aldehyde dehydrogenase
Query= curated2:Q87L22 (485 letters) >FitnessBrowser__Putida:PP_0708 Length = 476 Score = 215 bits (547), Expect = 3e-60 Identities = 160/457 (35%), Positives = 231/457 (50%), Gaps = 18/457 (3%) Query: 2 THWIAGEWVQGQGEEFVSLS-PYNQEVIWRGNGATAEQVDQAVAAARAAFVEWKKRPFAE 60 +H+IAG WV+GQG + +S++ P + A+ QVDQAVAAAR+A WK +E Sbjct: 4 SHYIAGHWVEGQGSDCISVNDPALGQPFAELMAASVSQVDQAVAAARSALPAWKSTCASE 63 Query: 61 REAIVLAFAEKVKENSEKIAEVIAKETGKPIWETRTE---AAAMAGKIAISIRAYHDRTG 117 R A + FAE++ + E + V + GKP E + A A G A + Sbjct: 64 RAAFLRGFAEQLGQRREALVTVQMRNNGKPRHEAEIDLDDAIATFGYYAELAEQLPSKNR 123 Query: 118 EATREAAGNQIVLRHRPLGVMAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSEQTPWTG 177 A G R P+GV+ + P+NFP + PAL AG TVV KPSE TP Sbjct: 124 TVPLAAPGFTARTRLEPVGVVGLIVPWNFPLVTSAWKLAPALAAGCTVVLKPSEVTPLIE 183 Query: 178 ELAMKLWEEAGLPKGVINLVQGAKETGIALADAKGIDGILFTGSANTGHILHRQFAGQPG 237 + ++ + GLP GV+N+V G ETG AL++ G+D + FTGS + G + R + Q Sbjct: 184 QAYGQIADALGLPAGVLNIVNGKAETGAALSNHNGLDKLSFTGSNSVGSQVMRSASAQ-C 242 Query: 238 KMLALEMGGNNPMVISDNYGDLDATVYTIIQSAFISAGQRCTCARRLYVPFGEKGDALIT 297 + + LE+GG + +V+ D+ D+D V I+ +AGQ C+ RL V G DAL+ Sbjct: 243 RPVTLELGGKSAIVVFDDC-DVDQAVEWIVAGISWNAGQMCSATSRLLVQDG-IADALLP 300 Query: 298 KLVEATKNIRMDQPFAEPAPFMGPQISVA-----AAKFILDAQANLQSLGGESLIEAKAG 352 +L A +N+R+ P E MGP S A A+ F + LQ L G ++ Sbjct: 301 RLQAALENLRVGNPLTEEVD-MGPLTSQAQWLKVASYFATAREEGLQCLAGGHALDR--- 356 Query: 353 EAAFVSPGI-IDVTNIAELPDEEYFGPLLQVVRYEGLDKAVELANDTRFGLSAGLVSTDD 411 E FVSP + DV + L EE FGP+L R+ ++A+ AND+RFGL A + S D Sbjct: 357 EGWFVSPTLYTDVPKDSRLWTEEIFGPVLCARRFATEEQAIAEANDSRFGLVATVCSADL 416 Query: 412 QEWEYFVDHIRAGIVNRNRQLTGASGDAPFGGPGASG 448 + E D + G V N + + +GG SG Sbjct: 417 ERAERVADALEVGHVWIN-SVQAVFVETSWGGTKGSG 452 Lambda K H 0.316 0.134 0.397 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: 611 Number of extensions: 29 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: 485 Length of database: 476 Length adjustment: 34 Effective length of query: 451 Effective length of database: 442 Effective search space: 199342 Effective search space used: 199342 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: 51 (24.3 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