Align N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized)
to candidate WP_110805920.1 C8J30_RS10945 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= curated2:Q2G9T9 (471 letters) >NCBI__GCF_003217355.1:WP_110805920.1 Length = 1127 Score = 198 bits (503), Expect = 9e-55 Identities = 160/457 (35%), Positives = 222/457 (48%), Gaps = 39/457 (8%) Query: 11 PATGAEVWRGKVGDVEEVVAR--ARRAWPAWAAQPLATRIELVRRFANEVRKDADNLATM 68 PATGA V R D V A R W A P A R ++ R A+ ++ + Sbjct: 553 PATGAVVARVTEADAATVAVALDAARVWSA----PAAERAAVLSRAADLYEENFGPIFAA 608 Query: 69 ISRETGKPLWEARTEVDSVVNKVEISIRAYADRTSQRKLDSALQGTAALRHKPHGVLAVL 128 ++RE GK L +A +E+ V+ +R YA +GT+ R P G + + Sbjct: 609 LAREAGKTLGDAISELREAVD----FLRYYA-----------AEGTSDTR-APRGPVVAI 652 Query: 129 GPYNFPAHLPNGHIVPALIAGNAVVFKPSEKTPATGEMLAQCFHRAGIPAAVVQVLIG-G 187 P+NFP + G I AL+AGNAV+ KP+E+TP + + H+AG+PA +Q+L G G Sbjct: 653 SPWNFPLAIFTGQIAAALMAGNAVLAKPAEQTPVIAALAVRLLHQAGVPATALQLLPGDG 712 Query: 188 PEEGQALVAHDGIDGVLFTGSAHAGIAINRKLASN--PGKIVALEMGGNNPIVVWDTPKI 245 P G AL I GV+FTGS I R +A++ PG + E GG N +VV T Sbjct: 713 PTVGAALTRDPRIKGVVFTGSTETAQIIARAMAAHMAPGTPLIAETGGLNAMVVDSTALP 772 Query: 246 EDAATLIVQSAFTSAGQRCTAARRLIIKASMFDEVIDHVKRLADRIIVGAPFDDPAPFMG 305 E A +V SAF SAGQRC+A R L ++ + VI +K D +++G P+ + +G Sbjct: 773 EQAVRDVVASAFRSAGQRCSALRCLYVQEDIAPHVIAMLKGAMDELVLGDPW-RLSTDVG 831 Query: 306 PVIDNRTADGLTESFVYLLSSGGRPIKHMVRLQEDRPFLSPAIIDVTAVADRPDVELFGP 365 PVID G+ YL + GR I H F++PA++ VT +AD E+FGP Sbjct: 832 PVIDAEAQAGIE---TYLAQNAGR-ILHRTAAPAGGHFVAPALLKVTGIADLSH-EIFGP 886 Query: 366 LLQVV--RVDDFDEAIAEANNTRFGLSASLIGGDPQDYNRFWANIRAGVVNWNRPTNGA- 422 +L + DD IA N +GL+ L IRAG + NR GA Sbjct: 887 VLHLATFAADDLPAVIAAINARGYGLTFGLHSRIDARVETVAETIRAGNIYVNRNQIGAV 946 Query: 423 SSAAPFGGVGLSGNHRPSA----YYAADYCAYPVAST 455 + PFGG GLSG P A Y Y PV +T Sbjct: 947 VGSQPFGGEGLSGT-GPKAGGPLYLGRFYAPEPVVAT 982 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: 1253 Number of extensions: 71 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: 1127 Length adjustment: 40 Effective length of query: 431 Effective length of database: 1087 Effective search space: 468497 Effective search space used: 468497 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: 55 (25.8 bits)
This GapMind analysis is from Sep 24 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