Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate GFF4232 Psest_4305 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__psRCH2:GFF4232 Length = 497 Score = 582 bits (1500), Expect = e-170 Identities = 292/492 (59%), Positives = 361/492 (73%), Gaps = 4/492 (0%) Query: 6 LAYWQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSA 65 LA WQ +A L IE R FI GEY AAA+ F+ + PV LA++A + D +RA+++ Sbjct: 6 LADWQQRARDLHIEGRAFIQGEYCAAADGGQFDCISPVDGRVLAQVASCEQADAERAVAS 65 Query: 66 ARGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAA 125 AR F+ G WS +PAKRKAVL + ADL+EA+ EELALLETLD GKPI SL DIPGAA Sbjct: 66 ARAAFDAGSWSRLAPAKRKAVLIRFADLLEANREELALLETLDMGKPIGDSLAVDIPGAA 125 Query: 126 RAIRWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAG 185 RA+RW EAIDK+Y EVA T +L ++ REPVGV+AAIVPWNFPL++ CWKLGPALA G Sbjct: 126 RALRWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVAAIVPWNFPLMMACWKLGPALATG 185 Query: 186 NSVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGS 245 NSV+LKPSEKSPL+AIR+A LA +AG+P GVLNV+ G+GH G+AL+ H D+D + FTGS Sbjct: 186 NSVVLKPSEKSPLTAIRIAQLAIDAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGS 245 Query: 246 TRTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAG 305 TR KQL+ AG+SNMKRVWLEAGGKS NIVFAD PDLQ AA A A I +NQG+VC AG Sbjct: 246 TRVAKQLMIYAGESNMKRVWLEAGGKSPNIVFADAPDLQAAAQAAAGAIAFNQGEVCTAG 305 Query: 306 TRLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQ 365 +RLL+E SI + FL ++ + + W+PG+PLDPAT +G L+D ++V +I G G Sbjct: 306 SRLLVERSIRERFLPMVVEALKGWKPGNPLDPATNVGALVDTQQLNTVLGYIDAGRQAGA 365 Query: 366 LLLDGRNAGLAAAIG----PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDS 421 +L G L G PTIF VD +++EEIFGPVL V F S E+A+ +AND+ Sbjct: 366 QVLIGGQRTLEETGGLYVEPTIFDGVDNAMRIAQEEIFGPVLSVITFDSAEEAVAIANDT 425 Query: 422 QYGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALE 481 YGL AAVWT DLS+AHR +R L+AGSV+VN Y+ GDMT PFGG+KQSGNGRDKSLHA + Sbjct: 426 PYGLAAAVWTADLSKAHRTARALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFD 485 Query: 482 KFTELKTIWISL 493 K+TELK WI L Sbjct: 486 KYTELKATWIQL 497 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: 649 Number of extensions: 19 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