Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate WP_036264374.1 DL86_RS17780 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1974 (488 letters) >NCBI__GCF_000746085.1:WP_036264374.1 Length = 1033 Score = 172 bits (437), Expect = 4e-47 Identities = 140/456 (30%), Positives = 210/456 (46%), Gaps = 22/456 (4%) Query: 35 ATAGQVESAVQAARQAFPDWARRTLEERISVLEAFAAALKNHADELAHTIGEETGKPLWE 94 A G ++ A++ AR F W+R + R + L+ A L+ A H + E GK L + Sbjct: 574 AAPGLLQEAMREARGGFKIWSRTPVGLRAACLDRAAQELEAQAPRWLHLLQIEAGKTLED 633 Query: 95 AATEVTSMVNKIAISVQSYRERTGEKS---GPLGDATAVLRHKPHGVVAVFGPYNFPGHL 151 A E ++ Q R R + GP G+ + H GV P+NFP + Sbjct: 634 AIGEWREAIDFCRYYAQEARRRFASPAPMPGPTGEDNRLFCHG-RGVFVCISPWNFPLSI 692 Query: 152 PNGHIVPALLAGNSVLFKPSELTPKVAELTVKCWIEAGLPAGVLNLLQGARETGIALAAN 211 G I AL AGNSVL KP+E TP +A V AG+PA VL+LL G + G AL A Sbjct: 693 FLGQIAAALAAGNSVLAKPAEQTPLIAAQAVSLLYRAGVPASVLHLLPGDGDVGAALVAL 752 Query: 212 PGIDGLFFTGSSRTGNHLHQQFAGRPDKI--LALEMGGNNPLVVDQVADLDAAVYTIIQS 269 G+ G+ TGS T +++ A + I L E GG N ++ D A + ++ S Sbjct: 753 DGVAGVAITGSMDTATKINRSLAAKSGPIAQLIAETGGVNAMIADATALPEQVCDDVVAS 812 Query: 270 AFISAGQRCTCARRLLVPQGAWGDSLLARLVAVSSTLSVGAFDQQPAPFMGSVVSLGAAK 329 AF SAGQRC+ A RLL Q D ++A + + L VG + +G V+ L A + Sbjct: 813 AFRSAGQRCS-ALRLLCLQEDVADRMIAMIKGAARELLVGD-PRALGVHVGPVIDLAAKR 870 Query: 330 ALMDAQEHLLANGAVALLEMTQPQAQSA-----LLTPGILDVSAVADRPDEELFGPLLQV 384 +L + H+ A A++ +A L P I ++S+V+D E FGP+L V Sbjct: 871 SL---EAHIEDMRACAIVHYAGRAPSTAPPRGFYLAPHIFELSSVSDL-RREAFGPILHV 926 Query: 385 IRY--ADFEAAIAEANDTAYGLAAGLLSDSEARYQQFWLESRAGIVNWNKQLTGA-ASSA 441 RY ++ + +GL G+ S +A + AG N+ + GA + Sbjct: 927 ARYKASELGGLLDSIEAAGFGLTLGVHSRIDAVIDEIVERRLAGNCYVNRNMIGAVVGTQ 986 Query: 442 PFGGVGASGN--HRASAYYAADYCAYPVASLETPSL 475 PFGG G SG +Y +C ++ T ++ Sbjct: 987 PFGGFGLSGTGPKAGGPHYLDRFCVEQTVTINTAAV 1022 Lambda K H 0.316 0.132 0.388 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: 1082 Number of extensions: 57 Number of successful extensions: 5 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: 488 Length of database: 1033 Length adjustment: 39 Effective length of query: 449 Effective length of database: 994 Effective search space: 446306 Effective search space used: 446306 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 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