Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate BWI76_RS10695 BWI76_RS10695 aldehyde dehydrogenase PuuC
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Koxy:BWI76_RS10695 Length = 495 Score = 824 bits (2129), Expect = 0.0 Identities = 405/495 (81%), Positives = 444/495 (89%) Query: 1 MNFHHLAYWQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDID 60 M+FH+LAYWQ KA L IE RLFINGEY+AAA+N F T+DP Q LA++ARGK D+D Sbjct: 1 MDFHNLAYWQQKARELTIETRLFINGEYSAAADNSVFATIDPAAQQTLAEVARGKKADVD 60 Query: 61 RAMSAARGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDD 120 RA+ AARGVF+RGDWS +SPA+RKAVL K ADLM+AH EELALLETLDTGKPIRHSLRDD Sbjct: 61 RAVQAARGVFDRGDWSQASPAQRKAVLTKFADLMDAHREELALLETLDTGKPIRHSLRDD 120 Query: 121 IPGAARAIRWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGP 180 IPGAARAIRWYAEAIDKVYGEVA T +ELAMIVREP+GVIAA+VPWNFPLLL CWKLGP Sbjct: 121 IPGAARAIRWYAEAIDKVYGEVAPTGGNELAMIVREPIGVIAAVVPWNFPLLLACWKLGP 180 Query: 181 ALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAI 240 ALA+GNSV+LKPSEKSPL+A+RLAGLAK+AGLPDGV NVV+GFGHEAGQAL+ H D++ I Sbjct: 181 ALASGNSVVLKPSEKSPLTALRLAGLAKQAGLPDGVFNVVSGFGHEAGQALALHPDVEVI 240 Query: 241 AFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQ 300 FTGSTRT KQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQ+A +ATA GIFYNQGQ Sbjct: 241 TFTGSTRTAKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQKAVNATAGGIFYNQGQ 300 Query: 301 VCIAGTRLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREG 360 VCIAGTRLLLEESIAD FL LLK+QA+ WQPG+PLDP TTMG LID HADSVHSFIR G Sbjct: 301 VCIAGTRLLLEESIADRFLDLLKEQAKGWQPGNPLDPNTTMGMLIDNTHADSVHSFIRAG 360 Query: 361 ESKGQLLLDGRNAGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLAND 420 E+ LLLDGR AA+GPTIFVDVDP + LS+EEIFGPVLVVTRF +EEQAL LAND Sbjct: 361 EAHSTLLLDGRKNPWPAAVGPTIFVDVDPASPLSQEEIFGPVLVVTRFKNEEQALALAND 420 Query: 421 SQYGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHAL 480 S+YGLGAAVWTRDLSRAHR+SRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHAL Sbjct: 421 SRYGLGAAVWTRDLSRAHRVSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHAL 480 Query: 481 EKFTELKTIWISLEA 495 EKFTELKTIWI+LE+ Sbjct: 481 EKFTELKTIWIALES 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: 767 Number of extensions: 11 Number of successful extensions: 1 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: 495 Length adjustment: 34 Effective length of query: 461 Effective length of database: 461 Effective search space: 212521 Effective search space used: 212521 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 Apr 09 2024. 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