Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate GFF3406 PS417_17430 aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__WCS417:GFF3406 Length = 506 Score = 336 bits (861), Expect = 1e-96 Identities = 192/483 (39%), Positives = 277/483 (57%), Gaps = 16/483 (3%) Query: 23 FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82 +I GE+ A E F PVT +A+ R + DID+A+ AA + W +SP Sbjct: 22 YIGGEFVAPLSGEYFTNTSPVTGEVIAEFPRSNAADIDKALDAAHAAADA--WGKTSPQD 79 Query: 83 RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142 R VL K+AD +E H E LA+ E+ D GK +R +L D+P AA R++A I G Sbjct: 80 RSLVLLKIADRIEQHLEVLAVTESWDNGKAVRETLNADVPLAADHFRYFAGCIRAQEGGA 139 Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202 A + H A EP+GV+ I+PWNFPLL+ WKL PALAAGN ++LKP+E++PLS + Sbjct: 140 AEINEHTAAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCIVLKPAEQTPLSIMV 199 Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262 A L + LP GVLN+V GFG EAG+AL+ I IAFTGST G ++ A + N+ Sbjct: 200 FAELINDL-LPPGVLNIVQGFGREAGEALATSKRIAKIAFTGSTPIGAHIMHAAAE-NLI 257 Query: 263 RVWLEAGGKSANIVFADC----PDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEF 318 +E GGKS NI F D P + A+ F+NQG+VC +R L++ESI D+F Sbjct: 258 PSTVELGGKSPNIFFEDIMQAEPQFIEKAAEGLVLAFFNQGEVCTCPSRALVQESIYDDF 317 Query: 319 LALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNA----- 373 + ++ ++ + G+PLD T +G D + S+++ + +G LL G A Sbjct: 318 MKVVMKKIVKIKRGNPLDTETMVGAQASEQQYDKILSYLKIAQEEGAELLTGGAAERLEG 377 Query: 374 --GLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWT 431 I PT+ + + +EEIFGPV+ +T F E +AL +ANDS++GLGA +WT Sbjct: 378 DLSSGYYIQPTLLKGHN-KMRVFQEEIFGPVVGITTFKDEAEALAIANDSEFGLGAGLWT 436 Query: 432 RDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491 RD++RA+RM R +KAG V+ N Y+ FGGYK+SG GR+ L+ + + K + + Sbjct: 437 RDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRENHKMMLDHYQQTKNLLV 496 Query: 492 SLE 494 S + Sbjct: 497 SYD 499 Lambda K H 0.317 0.133 0.389 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: 541 Number of extensions: 20 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: 495 Length of database: 506 Length adjustment: 34 Effective length of query: 461 Effective length of database: 472 Effective search space: 217592 Effective search space used: 217592 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 (21.7 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