Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate GFF882 Psest_0905 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__psRCH2:GFF882 Length = 499 Score = 356 bits (913), Expect = e-102 Identities = 196/478 (41%), Positives = 286/478 (59%), Gaps = 11/478 (2%) Query: 22 LFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPA 81 LFI+ ++ + ET + ++P L I + D+DRA+ AA+ F W +SPA Sbjct: 19 LFIDNQWVSDEYGETLDIINPANGKILTNIPNATAADVDRAVQAAQRAFMT--WRTTSPA 76 Query: 82 KRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGE 141 +R L K+ADL+EA A+ A+LETLD GKPIR S DIP A R++A I E Sbjct: 77 ERANALLKIADLLEADADRFAVLETLDVGKPIRESRSVDIPLAIDHFRYFAGVIRSQSDE 136 Query: 142 VATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAI 201 L++ + EP+GV+ ++PWNFPLL+ WK+ PA+AAGN+V++KPSE +P++ + Sbjct: 137 AVMLDEQTLSIALSEPLGVVGQVIPWNFPLLMAAWKIAPAIAAGNTVVIKPSELTPVTIL 196 Query: 202 RLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNM 261 LA + + LP GV+N+VTG G GQAL H D+ +AFTGSTR G +L+ +A + Sbjct: 197 ELAKIFAKV-LPAGVVNIVTGLGTTVGQALLDHPDLRKLAFTGSTRVG-ELVANAAAKKI 254 Query: 262 KRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLAL 321 LE GGKSANIVF D + +A I +NQGQVC +G RL + ESI + FLA Sbjct: 255 IPATLELGGKSANIVFPDA-NWDKAVEGAVLAILWNQGQVCESGARLFVHESIYERFLAE 313 Query: 322 LKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLL------LDGRNAGL 375 LK + + + G PL+P T MG + + + + ++ + +G + L G N Sbjct: 314 LKHKFEAVRVGDPLNPDTMMGAQVSKSQMERILGYVDIAKQEGAEVLIGGGRLTGANYDA 373 Query: 376 AAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLS 435 I PTI V V + ++ EEIFGPVL V F E + + +ANDS+YGL AVWT+D++ Sbjct: 374 GFFIQPTILVGVRNDMRVAYEEIFGPVLCVIPFKDEAEVIAMANDSEYGLAGAVWTQDIN 433 Query: 436 RAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISL 493 RA R++R ++ G ++VN Y++ PFGGYK+SG GR+ LE +++ K I++SL Sbjct: 434 RALRVARAVETGRMWVNTYHEIPAHAPFGGYKKSGLGRETHKSMLEAYSQKKNIYVSL 491 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: 588 Number of extensions: 28 Number of successful extensions: 7 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: 499 Length adjustment: 34 Effective length of query: 461 Effective length of database: 465 Effective search space: 214365 Effective search space used: 214365 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