Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate CA265_RS19780 CA265_RS19780 aldehyde dehydrogenase family protein
Query= curated2:Q87L22 (485 letters) >FitnessBrowser__Pedo557:CA265_RS19780 Length = 513 Score = 187 bits (476), Expect = 6e-52 Identities = 136/448 (30%), Positives = 224/448 (50%), Gaps = 17/448 (3%) Query: 19 SLSPYNQEVIWRGNGATAEQVDQAVAAARAAFVEWKKRPFAEREAIVLAFAEKVKENSEK 78 S SP + ++I ATA+ D V A+ AF W+ P +R IV F + ++EN + Sbjct: 38 SFSPVDGKLIASAKIATADDYDAVVLKAQEAFTAWRSVPAPKRGEIVRQFGDALRENKDA 97 Query: 79 IAEVIAKETGKPIWETRTEAAAMAGKIAISIRAYHDRTGEATR-EAAGNQIVLRHRPLGV 137 + +++ E GK + E E M ++ G E +++ + PLG+ Sbjct: 98 LGTLVSYEMGKSLQEGFGEVQEMIDICDFAVGLSRQLYGLTMHSERPSHRMYEQWHPLGI 157 Query: 138 MAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSEQTPWTG----ELAMKLWEEAGLPKGV 193 + + +NFP + + + AL+ GN ++KPSE+TP T + K++++ + +GV Sbjct: 158 VGIISAFNFPVAVWSWNTALALVCGNVCIWKPSEKTPLTAIACQHIIAKVFKDNDIAEGV 217 Query: 194 INLVQGAKETGIALADAKGIDGILFTGSANTGHILHRQFAGQPGKMLALEMGGNNPMVIS 253 NL+ G +E G + + I I TGS G + + GK L LE+GGNN ++IS Sbjct: 218 CNLILGDREVGERMTNDGRIPLISATGSTRMGKAVGAAVGARLGKSL-LELGGNNAIIIS 276 Query: 254 DNYGDLDATVYTIIQSAFISAGQRCTCARRLYVPFGEKGDALITKLVEATKNIRMDQPFA 313 + + DLD ++ + A +AGQRCT RRL + DA KLV+A +R+ P Sbjct: 277 E-HADLDMSLIGAVFGAVGTAGQRCTSTRRLII-HESVYDAFTAKLVKAYGQLRIGDPL- 333 Query: 314 EPAPFMGPQISVAAAKFILDAQANLQSLGGESLIE--AKAGEA----AFVSPGIIDVTNI 367 + +GP I A LD+ A ++ GG ++E +G+A +V P I +V N Sbjct: 334 DQNNHVGPLIDTDAVAAYLDSIAKCKAEGGNFVVEGGVLSGDAYTSGCYVKPCIAEVQND 393 Query: 368 AELPDEEYFGPLLQVVRYEGLDKAVELANDTRFGLSAGLVSTDDQEWEYFVD--HIRAGI 425 ++ E F P+L +++Y+ LD+A+ L N GLS+ +++ + +E E F+ GI Sbjct: 394 FKIVQHETFAPILYLIKYKTLDEAIALQNGVPQGLSSAIMTLNLREAEQFLSAKGSDCGI 453 Query: 426 VNRNRQLTGASGDAPFGGPGASGNLRPS 453 N N +GA FGG +G R S Sbjct: 454 ANVNIGTSGAEIGGAFGGEKETGGGRES 481 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: 545 Number of extensions: 35 Number of successful extensions: 8 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: 513 Length adjustment: 34 Effective length of query: 451 Effective length of database: 479 Effective search space: 216029 Effective search space used: 216029 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