Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate 16751 b2661 succinate-semialdehyde dehydrogenase I, NADP-dependent (NCBI)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1974 (488 letters) >FitnessBrowser__Keio:16751 Length = 482 Score = 212 bits (539), Expect = 3e-59 Identities = 164/468 (35%), Positives = 229/468 (48%), Gaps = 24/468 (5%) Query: 6 IAGEWL-AGGGEAFESLNPVTQQVLWSGVGATAGQVESAVQAARQAFPDWARRTLEERIS 64 I GEWL A GEA + NP L S A + +A+ AA +A P W T +ER + Sbjct: 15 INGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRALPAWRALTAKERAT 74 Query: 65 VLEAFAAALKNHADELAHTIGEETGKPLWEAATEVTSMVNKIAISVQSYRERTGEK-SGP 123 +L + + H D+LA + E GKPL EA E++ + I + + G+ G Sbjct: 75 ILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEEGKRIYGDTIPGH 134 Query: 124 LGDATAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVLFKPSELTPKVAELTVK 183 D ++ +P GV A P+NFP + PAL AG +++ KP+ TP A + Sbjct: 135 QADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPFSALALAE 194 Query: 184 CWIEAGLPAGVLNLLQG-ARETGIALAANPGIDGLFFTGSSRTGNHLHQQFAGRPDKILA 242 I AG+PAGV N++ G A G L +NP + L FTGS+ G L +Q A + K ++ Sbjct: 195 LAIRAGVPAGVFNVVTGSAGAVGNELTSNPLVRKLSFTGSTEIGRQLMEQCA-KDIKKVS 253 Query: 243 LEMGGNNPLVVDQVADLDAAVYTIIQSAFISAGQRCTCARRLLVPQGAWGDSLLARLVAV 302 LE+GGN P +V ADLD AV + S F +AGQ C CA RL V G + D +L Sbjct: 254 LELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGVY-DRFAEKLQQA 312 Query: 303 SSTLSVGAFDQQPAPFMGSVVSLGA---AKALMDAQEHL---LANGAVALLEMTQPQAQS 356 S L +G + + V++G KA+ +EH+ L GA + + Sbjct: 313 VSKLHIG-------DGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAHERGG 365 Query: 357 ALLTPGIL-DVSAVADRPDEELFGPLLQVIRYADFEAAIAEANDTAYGLAAGLLSDSEAR 415 P IL DV A A EE FGPL + R+ D IA+ANDT +GLAA + +R Sbjct: 366 NFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYARDLSR 425 Query: 416 YQQFWLESRAGIVNWNKQLTGAASS--APFGGVGASGNHRASAYYAAD 461 + GIV N TG S+ APFGG+ ASG R + Y + Sbjct: 426 VFRVGEALEYGIVGIN---TGIISNEVAPFGGIKASGLGREGSKYGIE 470 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: 527 Number of extensions: 31 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: 488 Length of database: 482 Length adjustment: 34 Effective length of query: 454 Effective length of database: 448 Effective search space: 203392 Effective search space used: 203392 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 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