Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_017549143.1 C792_RS0108995 aldehyde dehydrogenase family protein
Query= BRENDA::Q88RC0 (480 letters) >NCBI__GCF_000330705.1:WP_017549143.1 Length = 501 Score = 325 bits (832), Expect = 3e-93 Identities = 182/473 (38%), Positives = 270/473 (57%), Gaps = 13/473 (2%) Query: 12 QAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALP--AWRALTA 69 + +INGE +++ +G T + NPATGEVI V + RA+ AA A W+ A Sbjct: 16 ELFINGEKVESSDGGTNDIINPATGEVIAKVAMATGEDAERAVMAARDAFENSKWKIYPA 75 Query: 70 KERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGD 129 +R+ L R +M E +L L GK + A G+I A E++A G Sbjct: 76 SKRAKILNRIASIMRERFKELVELEVLNSGKSINAATGQINQAVEDFEYYAGAVCNHGGQ 135 Query: 130 T--IPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPY 187 T +PG + K+P+GV A I PWN+P M K PALAAGCT+VLKPAS TP Sbjct: 136 TNDVPGQFHN---YTEKEPVGVCAQIVPWNYPLMMAAWKVAPALAAGCTVVLKPASLTPL 192 Query: 188 SALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAK 247 +AL L E+ AG+P GV++++ GS VG L + V K++FTGST+ G+ +M + ++ Sbjct: 193 TALILGEICQEAGVPDGVINILPGSGSRVGDYLVEHPEVDKVAFTGSTDTGKDIMSKASR 252 Query: 248 DIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAE 307 +K+++LELGG +P ++F DA+L+ AV ++ Y N GQ+C +RIYV+D +YD F E Sbjct: 253 TLKRLTLELGGKSPALIFGDAELENAVASSVYGIYNNTGQSCDARSRIYVEDRIYDKFVE 312 Query: 308 KLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLI-----E 362 + ++K+G+ + + T G LID + V+ +IE A +GA + GG + E Sbjct: 313 QFVEKTKQMKMGDPMSKETHMGSLIDKSQLESVEAYIETARQEGATIAYGGNRLSIEGYE 372 Query: 363 GNFF-EPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDM 421 G F+ EPTI+ DV + V ++E FGP+ + RF DE E ++++N+T +GLAS Y D Sbjct: 373 GGFWLEPTIITDVTEDMTVVRDEIFGPVVVISRFSDEKEAVSLANNTIYGLASSIYTEDT 432 Query: 422 SRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474 + RVA+ + G+V IN + PFGG K SG GRE S ++ Y E K Sbjct: 433 RKAKRVADKIRAGIVMINCPFSAFPGTPFGGYKQSGFGRELSAETLDLYSETK 485 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: 584 Number of extensions: 22 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: 501 Length adjustment: 34 Effective length of query: 446 Effective length of database: 467 Effective search space: 208282 Effective search space used: 208282 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 24 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