Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate PfGW456L13_3141 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3141 Length = 498 Score = 424 bits (1091), Expect = e-123 Identities = 211/482 (43%), Positives = 312/482 (64%), Gaps = 1/482 (0%) Query: 13 ALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFER 72 A L + F+NGE + TF T +P T LA+I + D+D A++ A+ FE Sbjct: 14 ARDLKFPTQSFVNGESYTSVSGNTFTTTNPATNDVLAEITACNAQDVDFAVAKAKEAFED 73 Query: 73 GDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYA 132 G W SP++RK VL + ADL+E ++ EL++LE+LD+GKP+R D+P IRW+A Sbjct: 74 GRWHKLSPSERKKVLLRFADLLEQNSHELSVLESLDSGKPVRECQLTDVPETIHMIRWHA 133 Query: 133 EAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKP 192 E IDK+Y A L+++VRE +GV+ ++PWNFPLL+ WK+GP+LAAG S+I+KP Sbjct: 134 ELIDKIYDSTAPVGPGALSLVVREAIGVVGLVLPWNFPLLMLAWKIGPSLAAGCSIIVKP 193 Query: 193 SEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQL 252 ++++ L+A+R+A LA EAG+P GV NV++G G E G+ L RH D+ ++FTGST TG++ Sbjct: 194 AKETTLTALRVAELAHEAGVPAGVFNVLSGGGGEVGEPLGRHMDVSMVSFTGSTATGRRF 253 Query: 253 LKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEE 312 L A DSN+KR+ LE GGK+ +V D DL AS G F+N G+ C A +RL++ Sbjct: 254 LNYAADSNLKRIVLECGGKNPAVVMNDVEDLDLVASHVVNGAFWNMGENCSASSRLIVHA 313 Query: 313 SIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRN 372 I DE L + Q + W+ G+PLDP +G ++ AH + V S++ + + ++ G N Sbjct: 314 DIKDELLKRIGVQMREWKMGNPLDPDNRLGAMVSKAHFEKVRSYLEQAAVEKLDVVYGGN 373 Query: 373 AGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTR 432 + PT+ V ++ L +EEIFGPVL VT F + ++A+ LANDS YGL A+V+T Sbjct: 374 TESDIFVEPTVVDGVGADSRLFQEEIFGPVLAVTTFNTVDEAIALANDSVYGLAASVYTD 433 Query: 433 DLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSG-NGRDKSLHALEKFTELKTIWI 491 +L A ++SR ++AG V VN + +GD + PFGGYK+SG GRDKS+ A +++TE+KTIWI Sbjct: 434 NLRNAIKLSREIRAGIVTVNCFGEGDASTPFGGYKESGFGGRDKSIWAHDQYTEIKTIWI 493 Query: 492 SL 493 + Sbjct: 494 DV 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: 591 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: 498 Length adjustment: 34 Effective length of query: 461 Effective length of database: 464 Effective search space: 213904 Effective search space used: 213904 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