Align N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized)
to candidate Synpcc7942_0489 Synpcc7942_0489 aldehyde dehydrogenase
Query= SwissProt::Q8ZPV0 (492 letters) >FitnessBrowser__SynE:Synpcc7942_0489 Length = 459 Score = 135 bits (341), Expect = 2e-36 Identities = 125/421 (29%), Positives = 191/421 (45%), Gaps = 27/421 (6%) Query: 40 AEACQAARAAFPRWARQPFAARQAIVEKFAALLEAHKAELTEVIARETGKPRWEA-ATEV 98 AE A +A F R + A R A ++ A L+ ++AEL + +A + KP EA A+E+ Sbjct: 10 AETLAALQATFDRGDTRTLAFRLARLQDLAKLVADNEAELLQALASDLRKPALEAYASEI 69 Query: 99 TAMINKIAISIKAYHARTGAQKSELV----DGAATLRHRPHGVLAVFGPYNFPGHLPNGH 154 + ++I ++ K +K + G A + P GV+ + GP+N+P L Sbjct: 70 YFVRDQIKLTCKHLRRWMQPEKQSISLMQQPGQAYRQAEPLGVVLIIGPWNYPFQLLITP 129 Query: 155 IVPALLAGNTLIFKPSELTPWTGETVIKLWERAGLPAGVLNLVQGGRETGQALSSLDDLD 214 ++ A+ AGN + KPSEL P T + +L P + +++G QAL + D Sbjct: 130 LIGAIAAGNCAVLKPSELAPATSSLIQRLISDRFDP-DYIRVLEGDASVSQALIT-QPFD 187 Query: 215 GLLFTGSASTGYQLHRQLSGQPEKI--LALEMGGNNPLIIEDAANIDAAVHLTLQSAFIT 272 + FTG + G + ++ E + + LE+GG +P I++ ++D A F Sbjct: 188 HIFFTGGTAIG---RKVMAAAAENLTPVTLELGGKSPCIVDTDIDLDVAARRIAWGKFFN 244 Query: 273 AGQRCTCARRLLVKQGAQGDAFLARLVDVAGRLQPGRWDDDPQPFIGGLISAQAAQHVME 332 AGQ C LLV Q + F+ L+D + + +DPQ SA A+ V + Sbjct: 245 AGQTCIAPDYLLV-QRTVAEPFIEALIDNIQQF----YGEDPQQ------SADYARIVSD 293 Query: 333 AWRQR--EALGGRTLLAPRKVKEGTSLLTPGIIELTGVAD-VPDEEVFGPLLNVWRYAHF 389 QR L T+ +V + P +I D + EE+FGPLL + Y Sbjct: 294 RHWQRLNSLLVDGTIRHGGQVDRSDRYIAPTLITDVNWRDPILQEEIFGPLLPILIYDQL 353 Query: 390 DEAIRLANNTRFGLSCGLVSTDRAQFEQLLLEARAGIVNWNKP-LTGAASTAPFGGVGAS 448 DEAI L+ L S DR E++L E AG V N L A FGGVG S Sbjct: 354 DEAIAQIRAQPKPLALYLFSRDRQVQERVLAETSAGSVCLNDTILQVGVPDAAFGGVGPS 413 Query: 449 G 449 G Sbjct: 414 G 414 Lambda K H 0.319 0.134 0.411 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: 487 Number of extensions: 25 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: 492 Length of database: 459 Length adjustment: 33 Effective length of query: 459 Effective length of database: 426 Effective search space: 195534 Effective search space used: 195534 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 51 (24.3 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