Align N-succinylglutamate 5-semialdehyde dehydrogenase 1; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase 1; SGSD 1 (uncharacterized)
to candidate Ga0059261_3926 Ga0059261_3926 L-proline dehydrogenase (EC 1.5.99.8)/delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12)
Query= curated2:Q12QD2 (498 letters) >FitnessBrowser__Korea:Ga0059261_3926 Length = 1199 Score = 183 bits (465), Expect = 3e-50 Identities = 153/475 (32%), Positives = 230/475 (48%), Gaps = 34/475 (7%) Query: 2 NQLEQLTPLTQTQFIAGQWLAGK----GPSFSSVNPANG-EVIWQGLGADAGQVDAAITS 56 N L +L + AG W A G S NPA+G +V+ + A+ + Sbjct: 543 NVLAELAASLKVSAAAG-WAAEPADRIGTSRPVYNPADGKDVVGTVVEVTPEAAQTAVAT 601 Query: 57 ARAAFYTWSAMSLTERLVIVEAFAEQLKEHAELFARTIALETGKALWESRTEVGAMTGKI 116 A+AA W+A++ ER ++ A+ +++ ++ I E GK+ + EV + Sbjct: 602 AQAAAADWAAVAPAERAACLDRAADIMQDRMQILMGLIIREAGKSAPNAIAEV-----RE 656 Query: 117 AIS-IKANAERTGTVENPMPGAKAFIRHKPHGVVAVFGPYNFPGHLPNGHIVPALIAGNT 175 AI ++ AE+ M GA HKP G V P+NFP + G + AL+AGNT Sbjct: 657 AIDFLRYYAEQA----RAMLGAA----HKPLGAVTCISPWNFPLAIFTGQVAAALVAGNT 708 Query: 176 VLFKPSELTPKVAELTMQLWQQAGLPNGVLNLLQGEIATGKALASHKGIDGLFFTGSSNT 235 VL KP+E TP +A + + +AG+P L L+ G+ G AL + G + FTGS+ Sbjct: 709 VLAKPAEETPLIAAQGVSILHEAGIPAAALQLVPGDGRIGAALVAAPGTQAVMFTGSTEV 768 Query: 236 GHLLHQQYA------GQPGKILALEMGGNNPLIITEVANVDAAVHDIIQSAFISSGQRCT 289 ++ ++ A G P +A E GG N +I+ A + V D+I SAF S+GQRC+ Sbjct: 769 ARIIQKELAKRLTDGGDPVPFIA-ETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCS 827 Query: 290 CARRLFIPKTANGDAILAKLLTSTAKIALGDPFAETQPFFGAMISDKAAAGMVKAQADIQ 349 R L + D IL L + ++++G + + G +I+ +A A + A + Sbjct: 828 ALRVLCLQDDV-ADRILVMLKGALHELSIGRTDSLSTD-IGPVITAEAKANIEGHIARML 885 Query: 350 AAG-GVSLIELTQVTPGLGFVTPGIIDVTDASPLADEEHFGPLLKVYRY--TDFDAAIDE 406 G GV IEL T FV P II++ + L + E FGP+L V RY D D ID Sbjct: 886 GMGRGVEQIELAGETAQGTFVPPTIIELQSIADL-EREVFGPVLHVVRYKRRDLDRVIDA 944 Query: 407 ANNTSFGLSAGLLADSETDYQHFYRRIRAGIVNWNKPITGA-SSAAPFGGIGASG 460 N T +GL+ GL + H +R+ AG + N+ I GA PFGG G SG Sbjct: 945 INATGYGLTFGLHTRLDETIAHVSQRVEAGNLYINRNIIGAVVGVQPFGGRGLSG 999 Lambda K H 0.317 0.133 0.390 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: 1333 Number of extensions: 64 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 498 Length of database: 1199 Length adjustment: 41 Effective length of query: 457 Effective length of database: 1158 Effective search space: 529206 Effective search space used: 529206 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 (21.7 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