Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_011812184.1 VEIS_RS21780 aldehyde dehydrogenase family protein
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_000015565.1:WP_011812184.1 Length = 496 Score = 335 bits (859), Expect = 2e-96 Identities = 192/473 (40%), Positives = 282/473 (59%), Gaps = 12/473 (2%) Query: 23 FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82 FI+G Y A A + E+ DP + A+ A G V++D A+ AA+ WS ++PA+ Sbjct: 26 FIDGAYQAGATSAALESFDPGSGRVFAQFAAGGEVEVDAAVHAAKRALPA--WSETAPAE 83 Query: 83 RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142 R VL +A + HA+ LAL+E LD+GK + + + D+ G RA +YA A+DK+ G+ Sbjct: 84 RSRVLWAIAQQVRQHADRLALIECLDSGKRLGEA-QGDVRGVIRAFEYYAGAVDKMQGDS 142 Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202 + V EP+GV A I+PWN+P+ + PALAAG +V+ KP+E++PLSA+ Sbjct: 143 FPLGKDYIGFTVEEPIGVAAQIIPWNYPVGTAARGIAPALAAGCTVVAKPAEQTPLSALL 202 Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262 LA LA AGLP GVLNVVTG G AG AL H I I FTGS TG+++++ A D N+ Sbjct: 203 LAELASAAGLPAGVLNVVTGTGAAAGAALVAHPGIGHITFTGSVATGQRVMRAAAD-NVT 261 Query: 263 RVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALL 322 RV LE GGKS +V ADC D++QA I+ N GQ+C AG+RL++E + F+A L Sbjct: 262 RVLLELGGKSPLVVLADC-DVEQALDGVLGAIYENAGQICSAGSRLIIERKLHGSFMARL 320 Query: 323 KQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRN-AGLAAAIG- 380 ++ GH LD +G + H + +H + ++G +L G + A A A G Sbjct: 321 LERVGKLGLGHGLD-QPDVGPVNSLLHLNRIHEHVATAAARGNAVLAGGSIAQPANAPGG 379 Query: 381 ----PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSR 436 PT+ + +EEIFGPVLVV + EQA+ LAN + Y L A ++TRD+++ Sbjct: 380 WFYRPTVIEARSAQDPVVQEEIFGPVLVVQQADDLEQAIALANGTDYALVAGIYTRDITQ 439 Query: 437 AHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTI 489 A+R +RR+ AG V++N Y G + VPFGG ++SG GR+K L ++ + +LK++ Sbjct: 440 AYRFARRVDAGQVYINEYFAGGIEVPFGGNRKSGFGREKGLEGIKSYCKLKSV 492 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: 600 Number of extensions: 25 Number of successful extensions: 6 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 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