Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate WP_011384888.1 AMB_RS12610 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1974 (488 letters) >NCBI__GCF_000009985.1:WP_011384888.1 Length = 1039 Score = 167 bits (423), Expect = 2e-45 Identities = 134/436 (30%), Positives = 203/436 (46%), Gaps = 17/436 (3%) Query: 26 QQVLWSGVGATAGQVESAVQAARQAFPDWARRTLEERISVLEAFAAALKNHADELAHTIG 85 ++V+ V A+ VE+A+ +AR AFP W E R S+LE A L+ Sbjct: 567 RRVVGEVVDASPADVEAALASARAAFPAWDDLGGEARASILERAADRLEADRARFMALAI 626 Query: 86 EETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK---SGPLGDATAVLRHKPHGVVAVF 142 E GK + +A +EV V+ + R R + GP+G++ ++ GV A Sbjct: 627 REAGKTIPDALSEVREAVDFLRFYAAEARARFSQPVRLPGPVGESNELMLGG-RGVFACI 685 Query: 143 GPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAELTVKCWIEAGLPAGVLNLLQGAR 202 P+NFP + G + AL AGN+V+ KP+ TP +A V+ +AG+P L+L+ G Sbjct: 686 SPWNFPLAIFVGQVAAALAAGNAVVAKPAPQTPLMAAAAVRLLHQAGVPPQALHLVPGGP 745 Query: 203 ETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGR--PDKILALEMGGNNPLVVDQVADLD 260 G AL NP +D + FTGS+ T H+++ A P L E GG N ++VD A + Sbjct: 746 AIGEALTVNPLVDAIAFTGSTATARHINRLRAAMDGPLAPLIAETGGLNAMIVDSSALPE 805 Query: 261 AAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLLARLVAVSSTLSVGAFDQQPAPF-- 318 V ++SAF SAGQRC+ R + + AW + L + LS+G PA Sbjct: 806 QVVADCLESAFRSAGQRCSALRVAFIQREAW-TRIQPLLAGAMAELSLG----DPALLST 860 Query: 319 -MGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSALLTPGILDVSAVADRPDEEL 377 +G V+ + + L+ L G + P + + D E+ Sbjct: 861 DVGPVIDEASRRRLLAHGGRLRHAGRMIGQSACPPDCRVGTFFAPMAHQLDNLDLLQSEV 920 Query: 378 FGPLLQVIRY--ADFEAAIAEANDTAYGLAAGLLSDSEARYQQFWLESRAGIVNWNKQLT 435 FGP+L VI + E + T+YGL G+ S +A Q +R G + N+ + Sbjct: 921 FGPILHVIPWEAGRLEQVLDCVAATSYGLTLGIHSRIDATIAQVIARARIGNIYVNRTMI 980 Query: 436 GA-ASSAPFGGVGASG 450 GA S PFGG+G SG Sbjct: 981 GAVVGSQPFGGLGLSG 996 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: 1116 Number of extensions: 56 Number of successful extensions: 6 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: 488 Length of database: 1039 Length adjustment: 39 Effective length of query: 449 Effective length of database: 1000 Effective search space: 449000 Effective search space used: 449000 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