Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate Ac3H11_1486 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase (EC 1.2.1.60)
Query= BRENDA::Q88RC0 (480 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1486 Length = 485 Score = 328 bits (840), Expect = 3e-94 Identities = 194/480 (40%), Positives = 273/480 (56%), Gaps = 15/480 (3%) Query: 10 RQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTA 69 R Q I G+ ++ + + NPAT EV+ V G AE A+ AA A PAW L A Sbjct: 2 RIQHLIGGK--PVESREYFETVNPATQEVLAEVASGGAAEVHAAVAAAKDAFPAWAGLPA 59 Query: 70 KERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEA-KGEIAYAASFIEWFAEEAKRIYG 128 ER+ +R+ +L+ LA T + G+ + + K I AA +FAE R+ G Sbjct: 60 PERAKLVRKLGDLIAAEVPTLALTETKDTGQVIGQTGKALIPRAADNFYYFAEMCTRVDG 119 Query: 129 DTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYS 188 T P P + P+GV A I+PWN P T K PALA G T VLK + +P + Sbjct: 120 HTYP--TPTHLNYTLFHPVGVCALISPWNVPFMTSTWKVAPALAFGNTAVLKMSELSPLT 177 Query: 189 ALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKD 248 A L ELA AGIPAGVL+VV G + G L + VR +SFTGST G ++++ A Sbjct: 178 AARLGELALEAGIPAGVLNVVHGYGKDAGEPLCTHPDVRAISFTGSTATGNRIVQ--AAG 235 Query: 249 IKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEK 308 +KK S+ELGG +PF+VF DADLD+A++ A+ + NNG+ C +RI VQ +Y FAEK Sbjct: 236 LKKFSMELGGKSPFVVFADADLDRALDAALFMIFSNNGERCTAGSRILVQKSIYADFAEK 295 Query: 309 LAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGG--------KL 360 AA ++ +G+ L+E T GP+I +AKV+ +IE +GA +L GG L Sbjct: 296 FAARARRIVVGDPLDEKTIVGPMISQAHLAKVRSYIELGPKEGATLLCGGLGTPDLPAHL 355 Query: 361 IEGNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARD 420 +GNF PT+ DV +A+EE FGP+A L F+DEAE I ++ND ++GL+SY + + Sbjct: 356 QKGNFVLPTVFADVDNRMKIAQEEIFGPVACLIPFEDEAEAIRLANDIQYGLSSYVWTEN 415 Query: 421 MSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCISV 480 + R RVA +E GM +N+ + + PFGG K SG GREG + E +LE K + +S+ Sbjct: 416 IGRAHRVAAGIEAGMCFVNSQNVRDLRQPFGGTKGSGTGREGGTWSYEVFLEPKNIAVSM 475 Lambda K H 0.317 0.134 0.384 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: 617 Number of extensions: 27 Number of successful extensions: 5 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: 480 Length of database: 485 Length adjustment: 34 Effective length of query: 446 Effective length of database: 451 Effective search space: 201146 Effective search space used: 201146 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 (21.6 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