Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate GFF3742 PGA1_262p01460 aldehyde dehydrogenase
Query= reanno::SB2B:6938906 (486 letters) >FitnessBrowser__Phaeo:GFF3742 Length = 497 Score = 195 bits (496), Expect = 3e-54 Identities = 148/481 (30%), Positives = 233/481 (48%), Gaps = 34/481 (7%) Query: 5 INGQWLAGEGKEMQSKNPAN-GEVIWQGKAAVPAQVQAAVMAARDAQFEWFMLGFEGRQA 63 I G+WLAGE E++++NP++ +++ A Q++A + A+ AQ EW G E +QA Sbjct: 24 IAGEWLAGES-EVENRNPSDLSDLVGIFAQASADQLEATLDQAQVAQREWAAYGLERKQA 82 Query: 64 IVEAYRNELEANKAELAEVIAQETGKPRWETATEAAAMIGKIGLSVSAYHKRTGTEVNEG 123 ++ A NE+ A EL ++++E GKP E + + G + Y ++ E Sbjct: 83 VLNAIGNEMMARAEELGTLLSREEGKP----LAEGKGEVYRAGQFFTYYAAECLRQIGEN 138 Query: 124 AAG-----RAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAE 178 A +R + G VA+ P+NFP + I PAL GN VV+KP+ +TP A Sbjct: 139 ADSVRPDIEVDVRREAVGTVAIISPWNFPTATASWKIAPALCYGNAVVWKPANITPASAV 198 Query: 179 LMLKLWEKAGLPAGVINLVQGEVET-GKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPG 237 + ++ E+ +P G+ +LV G + G+ L P+++ + FTGS G + + Sbjct: 199 ALAEIIERQDIPKGLFSLVMGSGRSIGQRLVESPKVNAISFTGSVPVGKGIASAAIQNLT 258 Query: 238 KILALEMGGNNPLIVKGVSDTRAAIHDIIQSAFISSGQRCTCARRLYVEKGAEGDKLLAG 297 K+ +EMG N L V +D A+ + AF +GQ+CT + RL V G D + Sbjct: 259 KV-QMEMGSKNALAVMDDADLDLAVTLALGGAFGGTGQKCTASSRLVVHAGIH-DAFVEK 316 Query: 298 LVEAVKAIKVG-PWNADPQPFMGSMISETAAKGMLDAQRNLLNLGAKSLVEMT------H 350 LV KA+KVG A Q MG ++SE L+ ++LG E+ Sbjct: 317 LVTGAKAMKVGHALEAGVQ--MGPVVSEQ----QLNENLAYVDLGKTEGAELACGGQRLE 370 Query: 351 LQAGTGLVSPGL-IDVTEVIELPDEEYFGPLLQVVRYTSFDEAIRLANDTRYGLSAGILA 409 + +SPG+ ++ T + + EE F PL V++ S+DEA+ + NDT +GL++GI+ Sbjct: 371 MPHQGFYMSPGVFLNTTNDMRINREEMFAPLTSVIKVGSYDEALSVVNDTNFGLTSGIVT 430 Query: 410 DDKADYEYFLARIRAGIVNWNKQITGASGAAPFGGVGASG------NHRASAFYAADYCA 463 A +F R G+V N G PFGG G S A+ FY A Sbjct: 431 QSLARATHFRRNARTGVVTVNLPTAGTDYHVPFGGRGDSSYGPREQGKAAAEFYTTVKTA 490 Query: 464 Y 464 Y Sbjct: 491 Y 491 Lambda K H 0.317 0.133 0.393 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: 544 Number of extensions: 22 Number of successful extensions: 5 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: 486 Length of database: 497 Length adjustment: 34 Effective length of query: 452 Effective length of database: 463 Effective search space: 209276 Effective search space used: 209276 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: 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