Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_011383248.1 AMB_RS04115 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase
Query= BRENDA::Q88RC0 (480 letters) >NCBI__GCF_000009985.1:WP_011383248.1 Length = 485 Score = 338 bits (868), Expect = 2e-97 Identities = 193/475 (40%), Positives = 279/475 (58%), Gaps = 16/475 (3%) Query: 15 INGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERSA 74 ING ++ TI NPA EVI + G AE +A+ AA +A P W L A +R+ Sbjct: 6 INGR--QVESASTIANLNPANNEVICQIAAGGEAEVAQAVAAAKEAFPKWAGLPASQRAK 63 Query: 75 KLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIA-YAASFIEWFAEEAKRIYGDTIPG 133 LR+ +L+ ++ D++A+L + + G+ K + AA +FA+ + G+T P Sbjct: 64 LLRKVGDLINQHVDEIAKLESLDTGQSYWRTKKMLVPRAADNFYFFADTCCHVDGETYPT 123 Query: 134 HQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALV 193 + D + QP+GV I+PWN P T K P LA G T VLK + +P SA L Sbjct: 124 N--DHLNYTLYQPVGVVGLISPWNVPFMTATWKTAPCLAFGNTAVLKMSELSPLSADRLG 181 Query: 194 ELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKVS 253 +L AGIPAGV ++V G VG L + VR +SFTGST G ++++ + +KK S Sbjct: 182 QLILEAGIPAGVFNIVHGYGSAVGEALVKHPDVRGVSFTGSTATGNRIIQ--SGGLKKYS 239 Query: 254 LELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAAV 313 +ELGG +P I+FDD D ++AV+ AI++ Y NNG++C RI VQDG+YD F LA Sbjct: 240 MELGGKSPNIIFDDCDFERAVDAAIVAVYGNNGESCTNGTRILVQDGLYDRFVAALAERT 299 Query: 314 AKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGG---------KLIEGN 364 K+ +G+ L+E T GP+I KV +IE +S+GA+V++GG L GN Sbjct: 300 RKVVVGDPLDEATNVGPMITRDHWKKVTSYIELGISEGARVVAGGLGTPEGLAPHLKNGN 359 Query: 365 FFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRV 424 F PT+L DV + VA+EE FGP+A + RFKDEAE + ++N T +GLASY + + +R Sbjct: 360 FVRPTVLADVDNSWRVAQEEIFGPVACVIRFKDEAEALKIANATSYGLASYVWTENGARA 419 Query: 425 FRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCIS 479 R+AE +E G+V +N+ + + PFGGIK SG GREG Y E +LE+K +C+S Sbjct: 420 IRMAEGIEAGLVFVNSQNVRDLRQPFGGIKGSGTGREGGHYSYEAFLEVKNVCVS 474 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: 644 Number of extensions: 27 Number of successful extensions: 4 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