Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::Q88RC0 (480 letters) >FitnessBrowser__Korea:Ga0059261_1680 Length = 469 Score = 285 bits (730), Expect = 2e-81 Identities = 163/451 (36%), Positives = 251/451 (55%), Gaps = 7/451 (1%) Query: 26 QTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERSAKLRRWFELMIE 85 +T V +PATG P TA+ A+ AA +A P W A ++R+A + + + Sbjct: 17 ETFPVIDPATGRPFADAPLASTADLDAAVAAARRAFPGWAATPIEDRAAAILAIADSIEA 76 Query: 86 NQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTIPGHQPDKRLIVIKQ 145 +D+LARL++ EQGKP+ A GEI A + W A + R+ V ++ Sbjct: 77 AKDELARLLSAEQGKPVPNAVGEIMGA---LAWARATAGLRPAVDVLKDDDSVRVEVHRK 133 Query: 146 PIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALVELAHRAGIPAGV 205 P+GV A+I+PWNFP + P L AG T+V+KP+S TP +AL +VE+A+ A +P GV Sbjct: 134 PLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTPLAALRMVEIAN-AHLPPGV 192 Query: 206 LSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKVSLELGGNAPFIVF 265 L+ VTG E+G + + + K+ FTGST GR +M + A ++K+++LELGGN IV Sbjct: 193 LNSVTGEV-EIGRAIASHPGIDKIVFTGSTPTGRSIMADGAANLKRLTLELGGNDAAIVL 251 Query: 266 DDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAAVAKLKIGNGLEEG 325 DAD+DK + N+GQ C R+YV + ++DA AEKLA +G G + Sbjct: 252 PDADVDKVAAKIFAKAFGNSGQICAAVKRVYVHESIHDALAEKLAEMARTAVVGPGSDAA 311 Query: 326 TTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIEGN--FFEPTILVDVPKTAAVAKE 383 + GP+ + K V+ +DA + G + L+GG+ EG+ FF +++VDV + E Sbjct: 312 SQFGPVQNRKQFDLVRALADDARAHGGRFLAGGEAREGDGYFFPLSVVVDVTDGMRIVDE 371 Query: 384 ETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVFRVAEALEYGMVGINTGLI 443 E FGP+ P+ R+ D + +A +N E GL ++ D + A+ LE G V +N Sbjct: 372 EQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPAAALAFAQRLEAGTVWVNDHAS 431 Query: 444 SNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474 + PFGG K SG+G E YG+E+Y++++ Sbjct: 432 ISPDVPFGGAKQSGVGTEFGLYGLEEYMQLQ 462 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: 566 Number of extensions: 31 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: 469 Length adjustment: 33 Effective length of query: 447 Effective length of database: 436 Effective search space: 194892 Effective search space used: 194892 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