Align Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized)
to candidate GFF374 Psest_0375 NAD-dependent aldehyde dehydrogenases
Query= SwissProt::Q9I6M5 (483 letters) >FitnessBrowser__psRCH2:GFF374 Length = 480 Score = 305 bits (781), Expect = 2e-87 Identities = 177/480 (36%), Positives = 260/480 (54%), Gaps = 5/480 (1%) Query: 6 AKLFRQQAYVDGAWVDADNGQTIKVNNPATGEIIGSVPKMGAAETRRAIEAADKALPAWR 65 A + R ++DG WV +D Q N ++IG + AA+ +AI AA +A PAW Sbjct: 2 ADVQRYDNFIDGQWVGSDRYQA-NTNPSDLSDVIGEYAQADAAQVEQAIAAARRAFPAWA 60 Query: 66 ALTAKERANKLRRWFDLMIENQDDLARLMTIEQGKPLAEAKGEIAYAASFLEWFGEEAKR 125 + RA+ L + ++ +++L L+ E+GK L EA GE+A A + ++F E R Sbjct: 61 TFGIQARADALEKVGLEILARREELGTLLAREEGKTLPEAIGEVARAGNIFKYFAGECLR 120 Query: 126 IYGDTIPGHQPDKRIIVIKQPIGVTAAITPWNFPSAMITRKAGPALAAGCTMVLKPASQT 185 G+T+ +P + V ++P+GV ITPWNFP A+ K PALA G +V+KPA Sbjct: 121 QAGETLQSVRPGVGVEVTREPLGVIGLITPWNFPIAIPAWKIAPALAFGNCVVIKPADLV 180 Query: 186 PYSALALAELAERAGIPKGVFSVVTGSAGEVGGELTSNPIVRKLTFTGSTEIGRQLMAEC 245 P A A+AE+ RAG P GVF++V G EVG + + V ++FTGS +GR + C Sbjct: 181 PGCAWAIAEIISRAGFPAGVFNLVMGKGREVGEAIVNAKDVDAVSFTGSVGVGRGIAQTC 240 Query: 246 AQDIKKVSLELGGNAPFIVFDDADLDAAVEGALISKYRNNGQTCVCANRLYVQDGVYDAF 305 KV LE+GG P IV DDADL+ AVE S + + GQ C ++R+ V +G+YD F Sbjct: 241 VARGAKVQLEMGGKNPQIVLDDADLNVAVELCTQSAFYSTGQRCTASSRIIVTEGIYDRF 300 Query: 306 VDKLKAAVAKLNIGNGLEAGVTTGPLIDAKAVAKVEEHIADAVSKGAKVVSGGKPHALG- 364 V+ + + K+ +G+ LE GV GP++ + + +I +GA++ GG+ G Sbjct: 301 VEAMVERIKKIKVGSALEQGVDVGPVVSEAQLEQDLRYIEIGKQEGARLACGGERVKCGT 360 Query: 365 -GTFFEPTILVDVPKNALVSKDETFGPLAPVFRFKDEAEVIAMSNDTEFGLASYFYARDL 423 G F PT+ VD N +S++E FGP+A V + KD E +AM+NDTEFGL++ L Sbjct: 361 EGYFLAPTLFVDSDPNMRISREEIFGPVANVVKVKDYDEALAMANDTEFGLSAGICTTSL 420 Query: 424 ARVFRVAEQLEYGMVGINTGLISNEV-APFGGIKASGLG-REGSKYGIEDYLEIKYLCLG 481 + GMV IN + PFGG K S G RE +Y E Y +K +G Sbjct: 421 KYANHFKRHAQAGMVMINLPTAGVDYHVPFGGRKGSSYGPREQGRYAQEFYTTVKTTYIG 480 Lambda K H 0.317 0.135 0.391 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: 590 Number of extensions: 27 Number of successful extensions: 3 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: 483 Length of database: 480 Length adjustment: 34 Effective length of query: 449 Effective length of database: 446 Effective search space: 200254 Effective search space used: 200254 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 (21.7 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