Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate WP_023430602.1 N177_RS02270 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::Q88RC0 (480 letters) >NCBI__GCF_000496075.1:WP_023430602.1 Length = 480 Score = 366 bits (939), Expect = e-105 Identities = 199/465 (42%), Positives = 277/465 (59%), Gaps = 4/465 (0%) Query: 15 INGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERSA 74 I+GEW A +G+TI V NPAT EVIG V A+ A+EA K W +A ER+ Sbjct: 12 IDGEWRPAASGKTIPVVNPATEEVIGKVAWAEKADLDAALEAVAKGFRVWSQTSAYERAK 71 Query: 75 KLRRWFELMIENQDDLARLMTTEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYGDTIPGH 134 +R+ L+ E D++A +MT EQGKP+AEA E A IEWFA EA+R+YG I Sbjct: 72 TMRKAAGLLRERADEIAAVMTLEQGKPVAEAMMETMAGADIIEWFAGEAQRVYGQIIAPR 131 Query: 135 QPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALVE 194 + +KQP+G AA TPWNFP + RK ALA GC++++K +TP + AL+ Sbjct: 132 AGGVTQLAMKQPVGPVAAFTPWNFPINQVVRKLSAALATGCSIIVKAPEETPAAPAALIR 191 Query: 195 LAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKVSL 254 AG+PAGV+++V G E+ L + ++RK+SFTGST +G+ L + +K+ ++ Sbjct: 192 AFVDAGVPAGVVNLVYGVPAEISEYLIPHPVIRKISFTGSTPVGKHLAALAGQHMKRATM 251 Query: 255 ELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAAVA 314 ELGG+AP IV +DAD+ KAV+ SK+RN GQ C+ R +QDGV F + A Sbjct: 252 ELGGHAPVIVTEDADVSKAVKLLAASKFRNAGQVCISPTRFLIQDGVKKDFLKGFTEAAK 311 Query: 315 KLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLI--EGNFFEPTILV 372 +K+GNGL+EGTT GPL + + V ++E I+DAV GA + +GG+ I +G F EPT++ Sbjct: 312 AVKVGNGLDEGTTMGPLANERRVPFLEELIQDAVDSGASLETGGRRIGNKGYFMEPTVIA 371 Query: 373 DVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVFRVAEALE 432 D P ++ V EE FGPLA + F D EVI +N +GLASY + + +E Sbjct: 372 DAPLSSRVMNEEPFGPLAVVNSFSDLDEVIEEANRLPYGLASYAFTGSQKTAHELTMRIE 431 Query: 433 YGMVGIN-TGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYL 476 GM IN GL EV PFGG+K SG G EG +E YL +++ Sbjct: 432 SGMTTINHIGLALPEV-PFGGMKDSGYGSEGGSEAVEPYLVTRFV 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: 607 Number of extensions: 22 Number of successful extensions: 2 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: 480 Length adjustment: 34 Effective length of query: 446 Effective length of database: 446 Effective search space: 198916 Effective search space used: 198916 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 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