Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate 203555 SO4480 aldehyde dehydrogenase (NCBI ptt file)
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__MR1:203555 Length = 506 Score = 325 bits (832), Expect = 3e-93 Identities = 191/483 (39%), Positives = 276/483 (57%), Gaps = 16/483 (3%) Query: 23 FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82 FI G++ A + F+ PV KI R + DI+ A+ AA + W +S + Sbjct: 22 FIGGKWVAPVNGKYFDNRSPVNGQNFCKIPRSDAQDIELALDAAHAA--KDAWGKTSVTE 79 Query: 83 RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142 R +L ++AD +E + E LA+ ET + GK +R +L D+P R++A I G Sbjct: 80 RSNILLRIADRVEQNLEYLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQEGSA 139 Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202 A + ++ EP+GV+ I+PWNFPLL+ WK+ PALAAGN V+LKP+E++P+S + Sbjct: 140 ADIDGNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQTPVSILV 199 Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262 L L ++ LP GVLNVV GFG EAGQAL+ I +AFTGST G +LK A +S + Sbjct: 200 LLELIEDL-LPPGVLNVVNGFGAEAGQALATSKRIAKLAFTGSTEVGFHILKCAAESLIP 258 Query: 263 RVWLEAGGKSANIVFADCPDLQQAASATAAG----IFYNQGQVCIAGTRLLLEESIADEF 318 +E GGKS N+ FAD D + A F+NQG+VC +R+L++ESI D F Sbjct: 259 ST-VELGGKSPNLYFADVMDQEDEYLDKAVEGMLLAFFNQGEVCTCPSRVLIQESIYDRF 317 Query: 319 LALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKG-QLLLDGRNAGLAA 377 + + +AQ + G+PLD AT +G D + S++ G+ +G Q+LL G L Sbjct: 318 IEKVLARAQTIKQGNPLDTATQVGAQASQEQFDKILSYLAIGKDEGAQVLLGGSLCQLEG 377 Query: 378 A------IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWT 431 I PTI + + +EEIFGPV+ VT F E +AL +AND++YGLGA VWT Sbjct: 378 EQSKGYYISPTIMKGHN-KMRIFQEEIFGPVISVTTFKDEAEALAIANDTEYGLGAGVWT 436 Query: 432 RDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491 RD++RA RM R ++AG V++N Y+ FGGYK+SG GR+ L + K + + Sbjct: 437 RDMNRAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLNHYQNTKNLLV 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: 540 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 Apr 09 2024. 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