Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate GFF3742 PGA1_262p01460 aldehyde dehydrogenase
Query= reanno::WCS417:GFF827 (481 letters) >FitnessBrowser__Phaeo:GFF3742 Length = 497 Score = 518 bits (1333), Expect = e-151 Identities = 254/473 (53%), Positives = 339/473 (71%) Query: 9 NYINGQWVAGADYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPAWSTSGIQARH 68 N I G+W+AG N NPS+LSD++G +A+A Q+ A +D A+ A W+ G++ + Sbjct: 22 NLIAGEWLAGESEVENRNPSDLSDLVGIFAQASADQLEATLDQAQVAQREWAAYGLERKQ 81 Query: 69 DALDKVGSEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYVPS 128 L+ +G+E++AR EELGTLL+REEGK L E GEV RAG F ++A ECLR G+ S Sbjct: 82 AVLNAIGNEMMARAEELGTLLSREEGKPLAEGKGEVYRAGQFFTYYAAECLRQIGENADS 141 Query: 129 VRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGCAWALA 188 VRP + V+V REA+G V +I+PWNFP A +WKIAPAL YGN VV KPA + P A ALA Sbjct: 142 VRPDIEVDVRREAVGTVAIISPWNFPTATASWKIAPALCYGNAVVWKPANITPASAVALA 201 Query: 189 EIISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVSCVSRQAKVQ 248 EII R P G+F+LVMGSGR +G LV SPKV+ ISFTGSV VG+ IA + + KVQ Sbjct: 202 EIIERQDIPKGLFSLVMGSGRSIGQRLVESPKVNAISFTGSVPVGKGIASAAIQNLTKVQ 261 Query: 249 LEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAGIHDQFVAAMAERM 308 +EMG KN ++DDADL AV L++ AF TGQ+CTASSRL+V AGIHD FV + Sbjct: 262 MEMGSKNALAVMDDADLDLAVTLALGGAFGGTGQKCTASSRLVVHAGIHDAFVEKLVTGA 321 Query: 309 KSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGLVTCDTEGYYLAPT 368 K++KVGHAL++G +GPVVS+ QL+++L Y+D+G++EGA L GG + +G+Y++P Sbjct: 322 KAMKVGHALEAGVQMGPVVSEQQLNENLAYVDLGKTEGAELACGGQRLEMPHQGFYMSPG 381 Query: 369 LFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSLKYANHFKR 428 +F ++ MRI+REE+F P+ +V++V Y+ AL++ NDT FGL++GI T SL A HF+R Sbjct: 382 VFLNTTNDMRINREEMFAPLTSVIKVGSYDEALSVVNDTNFGLTSGIVTQSLARATHFRR 441 Query: 429 HSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIGS 481 +++ G+V VNLPTAG DYHVPFGGR SSYG REQG+ A EFYT VKT+YI + Sbjct: 442 NARTGVVTVNLPTAGTDYHVPFGGRGDSSYGPREQGKAAAEFYTTVKTAYISA 494 Lambda K H 0.318 0.134 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: 571 Number of extensions: 13 Number of successful extensions: 1 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: 481 Length of database: 497 Length adjustment: 34 Effective length of query: 447 Effective length of database: 463 Effective search space: 206961 Effective search space used: 206961 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