Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_011911298.1 PST_RS00240 aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_000013785.1:WP_011911298.1 Length = 497 Score = 578 bits (1491), Expect = e-169 Identities = 290/491 (59%), Positives = 359/491 (73%), Gaps = 4/491 (0%) Query: 7 AYWQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAA 66 A WQ +A L IE R FI GEY AAA+ F+ + PV LA++A D +RA+++A Sbjct: 7 ADWQQRARDLRIEGRAFIQGEYCAAAQGGQFDCISPVDGRVLAQVASCDLADAERAVASA 66 Query: 67 RGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAAR 126 R FE G W+ +PAKRKAVL + ADL+EA+ EELALLETLD GKPI SL DIPGAAR Sbjct: 67 RAAFEAGSWAKLAPAKRKAVLIRFADLLEANREELALLETLDMGKPIGDSLTVDIPGAAR 126 Query: 127 AIRWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGN 186 A+RW EAIDK+Y EVA T +L ++ REPVGV+AAIVPWNFPL++ CWKLGPALA GN Sbjct: 127 ALRWSGEAIDKIYDEVAATPHDQLGLVTREPVGVVAAIVPWNFPLMMACWKLGPALATGN 186 Query: 187 SVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGST 246 SV+LKPSEKSPL+AIR+A LA +AG+P GVLNV+ G+GH G+AL+ H D+D + FTGST Sbjct: 187 SVVLKPSEKSPLTAIRIAQLAIDAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGST 246 Query: 247 RTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGT 306 R KQL+ AG+SNMKRVWLEAGGKS NIVFAD PDLQ AA A A I +NQG+VC AG+ Sbjct: 247 RVAKQLMIYAGESNMKRVWLEAGGKSPNIVFADAPDLQAAAQAAAGAIAFNQGEVCTAGS 306 Query: 307 RLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQL 366 RLL+E SI + FL ++ + + W+PG+PLDP+T +G L+D ++V +I G G Sbjct: 307 RLLVERSIKERFLPMVVEALKGWKPGNPLDPSTNVGALVDTQQLNTVLGYIDAGRQAGAQ 366 Query: 367 LLDGRNAGLAAAIG----PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQ 422 +L G L G PTIF VD +++EEIFGPVL V F S E+A+ +AND+ Sbjct: 367 VLIGGQRTLEETGGLYVEPTIFDGVDNAMKIAQEEIFGPVLSVISFDSAEEAVAIANDTP 426 Query: 423 YGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEK 482 YGL AAVWT DLS+AHR +R L+AGSV+VN Y+ GDMT PFGG+KQSGNGRDKSLHA +K Sbjct: 427 YGLAAAVWTADLSKAHRTARALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDK 486 Query: 483 FTELKTIWISL 493 +TELK WI L Sbjct: 487 YTELKATWIQL 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: 642 Number of extensions: 17 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 24 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