Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate PP_2589 PP_2589 Aldehyde dehydrogenase family protein
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Putida:PP_2589 Length = 497 Score = 496 bits (1278), Expect = e-145 Identities = 243/492 (49%), Positives = 342/492 (69%), Gaps = 4/492 (0%) Query: 6 LAYWQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSA 65 L +WQ +A L + I+G+ A + TF ++P T LA++A ++D A+++ Sbjct: 4 LEFWQQRASDLYLPAHALIDGKPVNAQDGATFAAINPATNNVLAQVAACGHAEVDLAVAS 63 Query: 66 ARGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAA 125 AR FE+G W +P +RK VL +LA+L+ AH EELALL++L+ GKP+ + D+PG+A Sbjct: 64 ARRAFEQGPWPRMAPGERKKVLLRLAELIMAHREELALLDSLNMGKPVMDAYNIDVPGSA 123 Query: 126 RAIRWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAG 185 WY EA+DK+Y +VA T+++ LA I RE +GV+AA+VPWNFPL + WKL PALAAG Sbjct: 124 HVFAWYGEALDKLYDQVAPTAANALATITREALGVVAAVVPWNFPLDMAAWKLAPALAAG 183 Query: 186 NSVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGS 245 NSV+LKP+E+SP SA+RLA LA EAG+P+GVLNVV G G +AGQAL H D+D + FTGS Sbjct: 184 NSVVLKPAEQSPFSALRLAQLALEAGVPEGVLNVVPGLGEQAGQALGLHPDVDCLVFTGS 243 Query: 246 TRTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAG 305 T+ GK ++ + SN+K+VWLE GGKS N+VF +C DL AA A GIF+NQG+VC A Sbjct: 244 TQVGKYFMQYSAQSNLKQVWLECGGKSPNLVFDNCQDLDLAAEKAAFGIFFNQGEVCSAN 303 Query: 306 TRLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVH-SFIREGESKG 364 +RL ++ +I DEF+ L+ +A+ W PG+PLDPA+ G ++D + + +R G+ Sbjct: 304 SRLYVQRAIHDEFIERLQAKARQWLPGNPLDPASRAGAIVDAGQTGRIEAAIVRAGQEGA 363 Query: 365 QLLLDGRNAGLAAA---IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDS 421 +L+ GR + + I PTIF V+ SL+REE+FGPVL V+ F +EE+A++LANDS Sbjct: 364 RLVCGGRRLTIEGSDNYIEPTIFAGVEGRMSLAREEVFGPVLAVSAFDTEEEAVRLANDS 423 Query: 422 QYGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALE 481 YGL A+VW+ D ++ HR++R LKAG+V VN + D+TVPFGG KQSG GRD SLH+ + Sbjct: 424 IYGLAASVWSDDFNQVHRVARALKAGTVSVNTVDALDVTVPFGGGKQSGFGRDLSLHSFD 483 Query: 482 KFTELKTIWISL 493 K+++LKT W L Sbjct: 484 KYSQLKTTWYQL 495 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: 629 Number of extensions: 22 Number of successful extensions: 2 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: 497 Length adjustment: 34 Effective length of query: 461 Effective length of database: 463 Effective search space: 213443 Effective search space used: 213443 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