Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate WP_085635633.1 MGEO_RS04980 NAD-dependent succinate-semialdehyde dehydrogenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1974 (488 letters) >NCBI__GCF_002115805.1:WP_085635633.1 Length = 476 Score = 190 bits (483), Expect = 8e-53 Identities = 143/461 (31%), Positives = 218/461 (47%), Gaps = 13/461 (2%) Query: 4 LYIAGEWLAGGG-EAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLEER 62 LYI G W++G E F+ LNP T++VL S A ++A+ AA A +WA RT ER Sbjct: 6 LYINGTWVSGASKERFDVLNPATEEVLASVASAEIADADAALDAAEAAMAEWAARTPRER 65 Query: 63 ISVLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIA-ISVQSYRERTGEKS 121 VL + ++ A I E GK +A E T + ++ R Sbjct: 66 SEVLRKAWELMTVRLEDFAKLITLENGKARTDAMGEATYAAEFFRWFAEEAVRADGLITH 125 Query: 122 GPLGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAELT 181 P A +++HKP G+ + P+N+P + I PAL AG +V+ KP+ TP Sbjct: 126 APASGARIMVQHKPAGLAVLVTPWNYPAAMGTRKIAPALAAGCAVIIKPASETPLTMLAL 185 Query: 182 VKCWIEAGLPAGVLNLLQGARETGIA--LAANPGIDGLFFTGSSRTGNHLHQQFAGRPDK 239 + EAG+P G++N+L R + + +P + + FTGS+ G L A D+ Sbjct: 186 MPLLEEAGVPPGLVNVLPSKRTGALVDHMLHDPRVRVVSFTGSTGVGRKLLHSAA---DQ 242 Query: 240 IL--ALEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLLA 297 +L A+E+GGN P+VV + AD+D A+ + + + G+ CT A R+ V + A ++ Sbjct: 243 VLKPAMELGGNAPVVVFEDADMDTAIEGTMLAKMRNLGEACTAANRIYVHE-AIAETFTK 301 Query: 298 RLVAVSSTLSVGAFDQQPAPFMGSVVSLGAAKALMDAQEHLLANGAVALLEMTQPQAQSA 357 RL S L VG P +G +V+ + + +A GA+ T P+ Sbjct: 302 RLTEKMSALKVGD-GIDPTVDVGPLVNAETRDKVAEFVADAVAKGAIIECGGTTPEGPGF 360 Query: 358 LLTPGIL-DVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEARY 416 P +L +V AD +E+FGP+ + + D E I ANDT YGL A + S R Sbjct: 361 YYPPTVLSNVPETADCVHDEIFGPVAAIQTFRDQEEVIRRANDTEYGLVAYVFSGDMKRA 420 Query: 417 QQFWLESRAGIVNWNKQLTGAASSAPFGGVGASGNHRASAY 457 Q G+V N+ L + +APFGG SG R + Sbjct: 421 LQVCERLDYGMVGLNRGLV-SDPAAPFGGTKQSGLGREGGH 460 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: 490 Number of extensions: 30 Number of successful extensions: 4 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: 476 Length adjustment: 34 Effective length of query: 454 Effective length of database: 442 Effective search space: 200668 Effective search space used: 200668 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: 52 (24.6 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