Align Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized)
to candidate Synpcc7942_0489 Synpcc7942_0489 aldehyde dehydrogenase
Query= SwissProt::Q9SAK4 (528 letters) >FitnessBrowser__SynE:Synpcc7942_0489 Length = 459 Score = 167 bits (423), Expect = 8e-46 Identities = 131/416 (31%), Positives = 203/416 (48%), Gaps = 27/416 (6%) Query: 118 LRRWYDL--LIAHKE-ELGQLITLEQGKPLKEAIGEVAY--------GASFIEYYAEEAK 166 L R DL L+A E EL Q + + KP EA Y + + + K Sbjct: 32 LARLQDLAKLVADNEAELLQALASDLRKPALEAYASEIYFVRDQIKLTCKHLRRWMQPEK 91 Query: 167 RVYGDIIPPNLSDRRLLVLKQPVGVVGAITPWNFPLAMITRKVGPALASGCTVVVKPSEL 226 + + P + R+ +P+GVV I PWN+P ++ + A+A+G V+KPSEL Sbjct: 92 QSISLMQQPGQAYRQA----EPLGVVLIIGPWNYPFQLLITPLIGAIAAGNCAVLKPSEL 147 Query: 227 TPLTALAAAELALQAGVPPGALNVVMGNAPEIGDALLTSPQVRKITFTGSTAVGKKLMAA 286 P T+ L + P + V+ G+A + AL+T P I FTG TA+G+K+MAA Sbjct: 148 APATSSLIQRL-ISDRFDPDYIRVLEGDA-SVSQALITQP-FDHIFFTGGTAIGRKVMAA 204 Query: 287 AAPTVKKVSLELGGNAPSIVFDDADLDVAVKGTLAAKFRNSGQTCVCANRVLVQDGIYDK 346 AA + V+LELGG +P IV D DLDVA + KF N+GQTC+ + +LVQ + + Sbjct: 205 AAENLTPVTLELGGKSPCIVDTDIDLDVAARRIAWGKFFNAGQTCIAPDYLLVQRTVAEP 264 Query: 347 FAEAFSEAVQKLEVGDGFRDGTTQGPLINDAAVQKVETFVQDAVSKGAKIIIGGKRHSLG 406 F EA + +Q+ G+ + +++D Q++ + + D I G + Sbjct: 265 FIEALIDNIQQF-YGEDPQQSADYARIVSDRHWQRLNSLLVDGT------IRHGGQVDRS 317 Query: 407 MTFYEPTVIRDVSDNMIMSKEEIFGPVAPLIRFKTEEDAIRIANDTIAGLAAYIFTNSVQ 466 + PT+I DV+ + +EEIFGP+ P++ + ++AI LA Y+F+ Q Sbjct: 318 DRYIAPTLITDVNWRDPILQEEIFGPLLPILIYDQLDEAIAQIRAQPKPLALYLFSRDRQ 377 Query: 467 RSWRVFEALEYGLVGVNEGLISTEV--APFGGVKQSGLGREGSKYGMDEYLEIKYV 520 RV G V +N+ ++ V A FGGV SG+G K + + K V Sbjct: 378 VQERVLAETSAGSVCLNDTILQVGVPDAAFGGVGPSGMGGYHGKASFETFSHYKLV 433 Lambda K H 0.317 0.134 0.383 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: 532 Number of extensions: 26 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: 528 Length of database: 459 Length adjustment: 34 Effective length of query: 494 Effective length of database: 425 Effective search space: 209950 Effective search space used: 209950 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