Align NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized)
to candidate 3607155 Dshi_0577 aldehyde dehydrogenase (RefSeq)
Query= metacyc::MONOMER-15736 (480 letters) >FitnessBrowser__Dino:3607155 Length = 483 Score = 310 bits (793), Expect = 9e-89 Identities = 180/472 (38%), Positives = 254/472 (53%), Gaps = 9/472 (1%) Query: 10 RQQAFIDGAWVDADNGQTIKVNNPA-TGEILGTVPKMGAAETRRAIEAADKALPAWRALT 68 R Q +IDGAW + I+ NP+ T +++G + A + A+ AA +A PAW A Sbjct: 4 RTQLYIDGAWTEGT--AQIENRNPSDTTDLIGMYAQADAGQLDTALAAARRAQPAWWAAG 61 Query: 69 AKERATKLRRWYELLIENQDDLGRLMTLEQGKPLAEAKGEIAYAASFIEWFAEEAKRIYG 128 ++R L L+ D++GRL++ E+GKPLAE KGE+ A F +FA EA R +G Sbjct: 62 IQKRHDVLMAIGTELMARSDEIGRLLSREEGKPLAEGKGEVYRAGQFFTYFAAEALRQHG 121 Query: 129 DVIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVIKPASQTPFS 188 D+ +P + V ++ +GV A I+PWNFP A K PALA G +V KPA+ TP S Sbjct: 122 DLAESVRPGIEIDVRREAVGVVAIISPWNFPVATPAWKIAPALAFGNAVVWKPANVTPAS 181 Query: 189 ALALVELAHRAGIPKGVLSVVTGSAGDIGGELTSNPIVRKLSFTGSTEIGRQLMAECAKD 248 A+AL E+ R IPKG+ ++V G D+G L + V +SFTGS +GR + A ++ Sbjct: 182 AIALTEIIARQDIPKGLFNLVAGPGRDVGQRLVESAEVDAISFTGSVPVGRGIAAAAVQN 241 Query: 249 IKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRLYIQDSVYDAFAEK 308 + KV +E+G P IV DD DLD AV A S + GQ C A+RL + +V+DAF EK Sbjct: 242 MTKVQMEMGSKNPLIVMDDCDLDLAVAHAASSAFGGTGQKCTAASRLIVHSAVHDAFVEK 301 Query: 309 LKAAVAKLKIGNGLEEGTTTGPLIDEKAVAKVQEHIADALKKGATLLAGGKSME----GN 364 L AA +K+G+ LE+GT GP++ E + + E+I +GA LL GG +E G Sbjct: 302 LVAAARAMKVGHALEDGTQLGPVVSESQLNQNMEYIGVGKDEGAELLCGGDRLEMATDGY 361 Query: 365 FFEPTILVNVPKDAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDLGRV 424 F P + D + +EE F P+ + R E +A +NDT+FGL + L R Sbjct: 362 FMAPAVFAGTANDMRINREEMFAPITAVQRVDSYDEALARANDTQFGLTAGIMTTSLARA 421 Query: 425 FRVAEALEYGMVGVNTGLISNEV-APFGGIKASGLG-REGSKYGIEDYLEIK 474 + G V VN + PFGG AS G RE Y E Y +K Sbjct: 422 SHFRAHMRAGCVMVNLPTAGTDYHVPFGGRGASSFGPREQGSYAAEFYTTVK 473 Lambda K H 0.317 0.135 0.390 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: 548 Number of extensions: 18 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: 480 Length of database: 483 Length adjustment: 34 Effective length of query: 446 Effective length of database: 449 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