Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate CA265_RS24850 CA265_RS24850 aldehyde dehydrogenase
Query= BRENDA::Q88RC0 (480 letters) >FitnessBrowser__Pedo557:CA265_RS24850 Length = 454 Score = 244 bits (624), Expect = 3e-69 Identities = 144/450 (32%), Positives = 233/450 (51%), Gaps = 5/450 (1%) Query: 28 IKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERSAKLRRWFELMIENQ 87 +++ NPAT E+I ++ + + + +A KA P W T +ER A + + +L+ Sbjct: 1 MQIINPATAEIITSLEEDNLSTLQLKFDALQKAQPQWAGKTLQERIAVITHFSDLLEVEI 60 Query: 88 DDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTIPGHQPDKRLIVIKQPI 147 + LA ++T+E GKPL +++ EI A + I+W A++ D + +P + I+ +P+ Sbjct: 61 EKLASVLTSEVGKPLQQSRNEINGARARIKWMLANAEKYLADEVMTDEPGIKEIIKYEPL 120 Query: 148 GVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALVELAHRAGIPAGVLS 207 GV I+ WN+P + PAL +G T++ KP+ + + + +L +AG+P V Sbjct: 121 GVVCNISAWNYPYLVGVNVFIPALLSGNTVMYKPSEYATLTGIEIEKLLKKAGVPDDVFH 180 Query: 208 VVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKVSLELGGNAPFIVFDD 267 + G A E G L N FTGS + G+ + E+ A + LELGG P + DD Sbjct: 181 IAIG-AKETGSALL-NMDFNGYFFTGSYKTGKLIYEKVAAKMVPCQLELGGKDPLYITDD 238 Query: 268 -ADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAAVAKLKIGNGLEEGT 326 D+ A G + NNGQ+C RIYVQ+ YD + V K G EG Sbjct: 239 VTDVAAAAIGTADGAFYNNGQSCCAVERIYVQEKNYDDYCNAFVTEVKSWKTGIPTAEGV 298 Query: 327 TTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIEGN--FFEPTILVDVPKTAAVAKEE 384 G L + ++ ++ ++DA++KGAK+L+GGK +EG +FEPT+L DV V +EE Sbjct: 299 YIGALTRKEQISVLENQVKDALNKGAKLLTGGKAVEGKGYYFEPTVLTDVTNDMLVMQEE 358 Query: 385 TFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVFRVAEALEYGMVGINTGLIS 444 +FGP+ + + KD+AE + M DT++GL + Y R ++ L+ G N Sbjct: 359 SFGPIIGIMKVKDDAEALKMMKDTDYGLTASVYTASQERAEKILAQLDAGSGYWNCCDRV 418 Query: 445 NEVAPFGGIKASGLGREGSKYGIEDYLEIK 474 + P+ G K SG+G S GI + + K Sbjct: 419 SAALPWSGRKYSGIGATLSHQGIRAFTKPK 448 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: 494 Number of extensions: 18 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: 454 Length adjustment: 33 Effective length of query: 447 Effective length of database: 421 Effective search space: 188187 Effective search space used: 188187 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: 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