Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate PfGW456L13_2360 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2360 Length = 496 Score = 385 bits (989), Expect = e-111 Identities = 219/480 (45%), Positives = 297/480 (61%), Gaps = 9/480 (1%) Query: 21 RLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSP 80 R+ I G++ AA+ +T +P T L + R D+DRA+ AAR F+ W+ + P Sbjct: 19 RMLIGGDWVEAADGQTMPLHNPATGEVLCVVPRATPEDVDRAVLAARQAFDDSAWTRTRP 78 Query: 81 AKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYG 140 +R+ +L KLADLM+ AE LA LE L+ GK + D+ A +R+ A K+ G Sbjct: 79 RERQNLLWKLADLMQRDAELLAQLECLNNGKSAAVAQVMDVQLAIDFLRYMAGWATKIEG 138 Query: 141 EVATTSSHEL------AMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSE 194 S+ + + I RE VGV+ AIV WNFPLLL CWKLGPALA G +V+LKP++ Sbjct: 139 STVDVSAPLMPNDQFHSFIRREAVGVVGAIVAWNFPLLLACWKLGPALATGCTVVLKPAD 198 Query: 195 KSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLK 254 ++PL+A++LA L EAG P+GV NVVTG G AG AL+ + +D + FTGST GKQ+ K Sbjct: 199 ETPLTALKLAELVLEAGYPEGVFNVVTGTGITAGSALTHNPLVDKLTFTGSTAVGKQIGK 258 Query: 255 DAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESI 314 A DS M RV LE GGKS IV AD DL+ AA+ A+ IF+NQGQVC AG+RL ++ Sbjct: 259 IAMDS-MTRVTLELGGKSPTIVMADA-DLKTAAAGAASAIFFNQGQVCCAGSRLYVQRKH 316 Query: 315 ADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREG-ESKGQLLLDGRNA 373 D +A + A + G+ LDP+ MG LI + V+ +I +G ES + G Sbjct: 317 FDNVVADISDIANAMKLGNGLDPSVDMGPLISARQQERVYGYIEKGRESGATIACGGEQF 376 Query: 374 GLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRD 433 G + PT+ VDVD SL +EEIFGPVLV F E AL++ANDS YGLGA++W+ D Sbjct: 377 GPGFFVKPTVIVDVDQKHSLVQEEIFGPVLVAIPFDDEADALRMANDSPYGLGASIWSND 436 Query: 434 LSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISL 493 L+ HRM R+K+GSV+VN ++ D +PFGGYK SG GR+ A+E +TELK++ I L Sbjct: 437 LAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREMGYAAIEHYTELKSVLIKL 496 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: 574 Number of extensions: 22 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: 495 Length of database: 496 Length adjustment: 34 Effective length of query: 461 Effective length of database: 462 Effective search space: 212982 Effective search space used: 212982 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