Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate GFF2074 PGA1_c21070 betaine aldehyde dehydrogenase BetB
Query= curated2:Q2G9T9 (471 letters) >FitnessBrowser__Phaeo:GFF2074 Length = 488 Score = 204 bits (520), Expect = 4e-57 Identities = 154/455 (33%), Positives = 222/455 (48%), Gaps = 16/455 (3%) Query: 4 AEIVSHEPATGAEVW----RGKVGDVEEVVARARRAW--PAWAAQPLATRIELVRRFANE 57 A S +PA+G EVW + DVE VA AR A+ P WA R +L+ R A+ Sbjct: 17 ARFESRDPASG-EVWAMMPEARASDVEAAVAAARAAFHAPDWAGMTATGRGKLLYRLADL 75 Query: 58 VRKDADNLATMISRETGKPLWEARTEVDSVVNKVEISIRAYADRTSQRKLDSALQGTAA- 116 + ++A+ LA + +R+TGK + E ++ V + AD+ L Sbjct: 76 IAENAETLAQLETRDTGKIIRETSAQIAYVADYYRY-YAGLADKIEGAHLPIDKPDMEVW 134 Query: 117 LRHKPHGVLAVLGPYNFPAHLPNGHIVPALIAGNAVVFKPSEKTPATGEMLAQCFHRAGI 176 LR +P GV+A + P+N L I PAL AG VV K SE+ PA A+ F +AG Sbjct: 135 LRREPLGVVAAVVPWNSQLFLAAVKIGPALAAGCTVVLKASEEAPAPLLEFARIFDQAGF 194 Query: 177 PAAVVQVLIG-GPEEGQALVAHDGIDGVLFTGSAHAGIAINRKLASNPGKIVALEMGGNN 235 P V+ V+ G G + G L AH GID + FTG + R A N +LE+GG + Sbjct: 195 PRGVLNVITGFGADCGAVLTAHPGIDHIAFTGGPDTARHVVRNSAENLAS-TSLELGGKS 253 Query: 236 PIVVWDTPKIEDAATLIVQSAFTSAGQRCTAARRLIIKASMFDEVIDHVKRLADRIIVGA 295 P +V++ I+ A V + F + GQ C A RLII + + + +K A+ I +GA Sbjct: 254 PFIVFEDVDIDSAVNAQVSAIFAATGQSCVAGSRLIISNQIKAQFLHRLKEKAENIRIGA 313 Query: 296 PFDDPAPFMGPVIDNRTADGLTESFVYLLSSGGRPIKHMVRLQEDRPFLSPAIIDVTAVA 355 P + P +GP+ + E L++G R + L+ + F P I+D + Sbjct: 314 P-ELPETEVGPLCTDAQMRRAVELVAASLAAGARIVTGGQPLEGEGNFFPPTILDCSEAP 372 Query: 356 DRPDV--ELFGPLLQVVRVDDFDEAIAEANNTRFGLSASLIGGDPQDYNRFWANIRAGVV 413 + P + E FGP+L V D EA+A AN+T GL++ + D +R IRAG+V Sbjct: 373 EAPCLREEFFGPVLSVCGFDTEAEALALANDTAHGLASGVFTRDLTRAHRMIRGIRAGIV 432 Query: 414 NWNRPTNGASSAAPFGGVGLSGNHRPSAYYAA-DY 447 W S APFGG GLSG+ R AA DY Sbjct: 433 -WVNTYRAVSPIAPFGGQGLSGHGREGGLQAALDY 466 Lambda K H 0.319 0.135 0.403 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: 599 Number of extensions: 40 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: 471 Length of database: 488 Length adjustment: 34 Effective length of query: 437 Effective length of database: 454 Effective search space: 198398 Effective search space used: 198398 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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