Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate RR42_RS21485 RR42_RS21485 aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Cup4G11:RR42_RS21485 Length = 454 Score = 408 bits (1048), Expect = e-118 Identities = 201/447 (44%), Positives = 295/447 (65%), Gaps = 1/447 (0%) Query: 48 LAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETL 107 L +I ++D+D A++ A+ FE G W SPA+ KA L + ADL+E HA ELA++E+L Sbjct: 1 LPEITACDALDVDIAVAKAKAAFEDGRWHRRSPAQCKATLLRFADLLEQHAHELAVMESL 60 Query: 108 DTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPW 167 D+GKPIR D+P IRW+AE IDK+Y A S+ L+++VREP+GV+ ++PW Sbjct: 61 DSGKPIRECQATDVPETIHTIRWHAELIDKIYDSTAPVGSNALSLVVREPIGVVGLVLPW 120 Query: 168 NFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEA 227 NFPLL+ WK+GP+LAAG S+I+KP++++ L+A+R+A LA EAG+P GV NV+ G G + Sbjct: 121 NFPLLMLAWKIGPSLAAGCSIIVKPAKETTLTALRVAELAHEAGVPAGVFNVLPGGGKDV 180 Query: 228 GQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAA 287 G+ L +H D+ ++FTGST TG+ L+ A DSN+KR+ LE GGK+ +V D D+ A Sbjct: 181 GEPLGKHMDVSMVSFTGSTDTGRLFLRYAADSNLKRIVLECGGKNPAVVMNDVEDIDVVA 240 Query: 288 SATAAGIFYNQGQVCIAGTRLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDC 347 G F+N G+ C A +RL++ + D LA + + W+ G PLDP +G+L+ Sbjct: 241 QHVVNGAFWNMGENCSASSRLIVHAEVKDNLLAHIGVHLREWKMGDPLDPEHRIGSLVSE 300 Query: 348 AHADSVHSFIREGESKGQLLLDGRNAGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTR 407 +H S+I ++ + G + PT+ V ++ L +EEIFGP+L VT Sbjct: 301 SHFRKGQSYIELANAENLRVAFGGGTEGETFVEPTVVDGVGQHSRLFKEEIFGPILSVTT 360 Query: 408 FTSEEQALQLANDSQYGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYK 467 FTS E+A+ LANDS YGL A+V+T +L+ A R+SR ++AG V VN + +GD+T PFGGYK Sbjct: 361 FTSTEEAIALANDSVYGLAASVYTSNLNNAIRLSREIRAGVVTVNCFGEGDVTTPFGGYK 420 Query: 468 QSG-NGRDKSLHALEKFTELKTIWISL 493 +SG GRDKS+ A +++TE+KTIWI + Sbjct: 421 ESGFGGRDKSIWAHDQYTEIKTIWIDV 447 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: 550 Number of extensions: 26 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: 454 Length adjustment: 33 Effective length of query: 462 Effective length of database: 421 Effective search space: 194502 Effective search space used: 194502 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: 51 (24.3 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