Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate 5208103 Shew_0615 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq)
Query= curated2:Q87L22 (485 letters) >FitnessBrowser__PV4:5208103 Length = 1059 Score = 182 bits (462), Expect = 5e-50 Identities = 151/469 (32%), Positives = 229/469 (48%), Gaps = 37/469 (7%) Query: 4 WIAGEWVQGQ---GEEFVSLSPYNQ-EVIWRGNGATAEQVDQAVAAARAAFVEWKKRPFA 59 W AG V G+ GE SPY+ +++ + A + ++QA+A+A AF W P Sbjct: 563 WSAGPIVNGETLSGETIEVKSPYDTTQIVGKVAFANNQAIEQALASAHNAFGSWCSTPVE 622 Query: 60 EREAIVLAFAEKVKENSEKIAEVIAKETGKPIWETRTEA----------AAMAGKIAISI 109 R + A+ ++EN E++ + +E GK I + E A A K+ Sbjct: 623 VRANALQKLADLLEENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKMMGKP 682 Query: 110 RAYHDRTGEATREAAGNQIVLRHRPLGVMAVFGPYNFPGHLPNGHIVPALLAGNTVVFKP 169 TGE N++ L+ R GV P+NFP + G + AL AGNTVV KP Sbjct: 683 ELLPGPTGEL------NELFLQGR--GVFVCISPWNFPLAIFLGQVTAALAAGNTVVAKP 734 Query: 170 SEQTPWTGELAMKLWEEAGLPKGVINLVQGAKET-GIALADAKGIDGILFTGSANTGHIL 228 +EQT G A++L EAG+PK + + G T G + + I G+ FTGS T + Sbjct: 735 AEQTSIVGYRAVQLAHEAGIPKEALQFLPGTGATVGATITADERIGGVCFTGSTVTAKRI 794 Query: 229 HRQFAGQPGKMLAL--EMGGNNPMVISDNYGDLDATVYTIIQSAFISAGQRCTCARRLYV 286 + A + G ++ L E GG N MV+ D+ + V ++ S+F SAGQRC+ R LY+ Sbjct: 795 NLTLAQRDGAIIPLIAETGGQNAMVV-DSTSQPEQVVNDVVSSSFTSAGQRCSALRVLYL 853 Query: 287 PFGEKGDALITKLVEATKNIRMDQPFAEPAPFMGPQISVAAAKFILDAQANLQSLGGESL 346 + D +I + A + + P + +GP I A AK L+A + G + Sbjct: 854 Q-EDIADRVIDVMKGAMDELTIGNPGSVKTD-VGPVID-ATAKANLNAHIDHIKQVGRLI 910 Query: 347 --IEAKAG--EAAFVSPGIIDVTNIAELPDEEYFGPLLQVVRYEGLD--KAVELANDTRF 400 +E AG FV+P +++ +I L ++E+FGP+L V+RY+ D K ++ N T F Sbjct: 911 NQLELPAGTENGHFVAPTAVEIDSIKVL-EKEHFGPILHVIRYKAADLPKVIDDINSTGF 969 Query: 401 GLSAGLVSTDDQEWEYFVDHIRAGIVNRNRQLTGA-SGDAPFGGPGASG 448 GL+ G+ S ++ D + G V NR GA G PFGG G SG Sbjct: 970 GLTLGIHSRNEGHALEVADKVNVGNVYINRNQIGAVVGVQPFGGQGLSG 1018 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: 1101 Number of extensions: 58 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: 1059 Length adjustment: 39 Effective length of query: 446 Effective length of database: 1020 Effective search space: 454920 Effective search space used: 454920 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: 55 (25.8 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