Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate Ac3H11_1486 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase (EC 1.2.1.60)
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1486 Length = 485 Score = 339 bits (870), Expect = 1e-97 Identities = 200/470 (42%), Positives = 278/470 (59%), Gaps = 21/470 (4%) Query: 35 ETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKRKAVLNKLADLM 94 E FETV+P TQ LA++A G + ++ A++AA+ F W+ +R ++ KL DL+ Sbjct: 16 EYFETVNPATQEVLAEVASGGAAEVHAAVAAAKDAFPA--WAGLPAPERAKLVRKLGDLI 73 Query: 95 EAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEVATTSSHELAMIV 154 A LAL ET DTG+ I + + IP AA ++AE +V G T +H L + Sbjct: 74 AAEVPTLALTETKDTGQVIGQTGKALIPRAADNFYYFAEMCTRVDGHTYPTPTH-LNYTL 132 Query: 155 REPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPD 214 PVGV A I PWN P + + WK+ PALA GN+ +LK SE SPL+A RL LA EAG+P Sbjct: 133 FHPVGVCALISPWNVPFMTSTWKVAPALAFGNTAVLKMSELSPLTAARLGELALEAGIPA 192 Query: 215 GVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSAN 274 GVLNVV G+G +AG+ L H D+ AI+FTGST TG ++++ AG +K+ +E GGKS Sbjct: 193 GVLNVVHGYGKDAGEPLCTHPDVRAISFTGSTATGNRIVQAAG---LKKFSMELGGKSPF 249 Query: 275 IVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALLKQQAQNWQPGHP 334 +VFAD DL +A A IF N G+ C AG+R+L+++SI +F +A+ G P Sbjct: 250 VVFADA-DLDRALDAALFMIFSNNGERCTAGSRILVQKSIYADFAEKFAARARRIVVGDP 308 Query: 335 LDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAAA-----------IGPTI 383 LD T +G +I AH V S+I G +G LL G GL + PT+ Sbjct: 309 LDEKTIVGPMISQAHLAKVRSYIELGPKEGATLLCG---GLGTPDLPAHLQKGNFVLPTV 365 Query: 384 FVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHRMSRR 443 F DVD +++EEIFGPV + F E +A++LAND QYGL + VWT ++ RAHR++ Sbjct: 366 FADVDNRMKIAQEEIFGPVACLIPFEDEAEAIRLANDIQYGLSSYVWTENIGRAHRVAAG 425 Query: 444 LKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISL 493 ++AG FVN+ N D+ PFGG K SG GR+ + E F E K I +S+ Sbjct: 426 IEAGMCFVNSQNVRDLRQPFGGTKGSGTGREGGTWSYEVFLEPKNIAVSM 475 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: 571 Number of extensions: 31 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: 485 Length adjustment: 34 Effective length of query: 461 Effective length of database: 451 Effective search space: 207911 Effective search space used: 207911 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