Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate RR42_RS26255 RR42_RS26255 aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Cup4G11:RR42_RS26255 Length = 499 Score = 561 bits (1447), Expect = e-164 Identities = 280/492 (56%), Positives = 363/492 (73%), Gaps = 4/492 (0%) Query: 6 LAYWQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSA 65 LAYW+ +A +++I ++ +I+G + AA+ TFET++P T LA++A + D+DRA++A Sbjct: 7 LAYWRKQAATVSIRSQAYIDGRWADAADGATFETINPATGKALARVAACGAQDVDRAVAA 66 Query: 66 ARGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAA 125 AR F+ G WS + + RKA L +L+ L+E H EELALLETLD GKPI +L+ DIP A Sbjct: 67 ARKAFQSGVWSDTPRSARKATLLRLSHLIETHREELALLETLDMGKPIAETLQYDIPEAG 126 Query: 126 RAIRWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAG 185 R WYAEAIDK+Y E+A T LA I REP+GV+AA+VPWN+PLL+ WK+ PALAAG Sbjct: 127 RTYAWYAEAIDKIYDEIAPTGPGVLATITREPLGVVAAVVPWNYPLLMASWKVAPALAAG 186 Query: 186 NSVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGS 245 NSV+LKP+E+SPL+A+RLA LA+EAG+P GV NVV G G AGQAL RH D+D IAFTGS Sbjct: 187 NSVVLKPAEQSPLTALRLAELAEEAGIPAGVFNVVPGLGAAAGQALGRHPDVDCIAFTGS 246 Query: 246 TRTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAG 305 T TGK+ ++ +G SN+KRVWLE GGKS +IVF DCPDL +AA A A GIF NQG++CIAG Sbjct: 247 TATGKRFMEYSGQSNLKRVWLECGGKSPHIVFDDCPDLDRAAQAAAIGIFSNQGEICIAG 306 Query: 306 TRLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQ 365 +RL ++ I D F+ L+ A QPG PLDPAT MG ++D A V S+++ GE +G Sbjct: 307 SRLYVQSGIYDAFMEKLEAHAARMQPGDPLDPATAMGAIVDGAQLQRVMSYVKSGEDEGA 366 Query: 366 LLLDGRNAGLAAAIG----PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDS 421 L G + G PTIF + ++ REEIFGPVL VTRF SEE+A+++ANDS Sbjct: 367 RLRAGGKRAHTDSGGFYMQPTIFECPTQSLTIVREEIFGPVLAVTRFESEEEAIRMANDS 426 Query: 422 QYGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALE 481 YGLG+ +WT +LSRAHR+SR+L+AG V+VN Y D D+TVPFGG KQSG+GRDKSLHAL+ Sbjct: 427 PYGLGSGLWTSNLSRAHRVSRKLQAGLVWVNCYMDSDVTVPFGGVKQSGSGRDKSLHALD 486 Query: 482 KFTELKTIWISL 493 K+T+LKT WISL Sbjct: 487 KYTDLKTTWISL 498 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: 640 Number of extensions: 19 Number of successful extensions: 3 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