Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate GFF3775 PGA1_262p01790 aldehyde dehydrogenase
Query= reanno::WCS417:GFF827 (481 letters) >FitnessBrowser__Phaeo:GFF3775 Length = 483 Score = 509 bits (1311), Expect = e-149 Identities = 255/473 (53%), Positives = 338/473 (71%) Query: 9 NYINGQWVAGADYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPAWSTSGIQARH 68 N I G WVAGA N NPS+L+D+IG +A+A Q++A ++ A+ A W+ GI+ ++ Sbjct: 7 NCIAGDWVAGATEIENRNPSDLNDLIGMFAQASPDQLDATLEQAQRAQVEWAGYGIERKY 66 Query: 69 DALDKVGSEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYVPS 128 + L +G+E++ R EELGTLLAREEGK L E GEV RAG F ++A E LR GD S Sbjct: 67 NVLMAIGTEMMTRAEELGTLLAREEGKPLAEGKGEVYRAGQFFTYYAAETLRQMGDTADS 126 Query: 129 VRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGCAWALA 188 VR G+ ++V RE +GVV +I+PWNFP A +WKIAPAL YGN VV KPA + P A AL Sbjct: 127 VRDGIEIDVRREPVGVVVVISPWNFPTATASWKIAPALCYGNAVVWKPANVTPASAVALV 186 Query: 189 EIISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVSCVSRQAKVQ 248 EII+R P G+ +LVMG+G +G LV SPKV+ ISFTGSV VG+ IA + +VQ Sbjct: 187 EIIARQDIPKGLVSLVMGAGSSIGQRLVESPKVNAISFTGSVPVGKGIAACAIQNLTRVQ 246 Query: 249 LEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAGIHDQFVAAMAERM 308 +EMG KN ++DDAD+ AV L++ AF +GQ+CTASSRL+V IHDQFV + Sbjct: 247 MEMGSKNALAVMDDADIDLAVSLALGGAFGGSGQKCTASSRLVVHQSIHDQFVEKLVMGA 306 Query: 309 KSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGLVTCDTEGYYLAPT 368 K++KVGHAL++GT +GPVVS+ QL+++L Y+D+ SEGA L+ GG + T+GYY++P Sbjct: 307 KAMKVGHALEAGTQMGPVVSEQQLNENLAYVDLAASEGAELLCGGQRLEMATDGYYVSPG 366 Query: 369 LFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSLKYANHFKR 428 +F + MRI+REE+F P+A V+ VA Y+ AL + NDT FGL+AGI TT+L A HF+R Sbjct: 367 IFVGTNNDMRINREEMFAPLACVIPVASYDEALHVVNDTNFGLTAGIVTTNLARATHFRR 426 Query: 429 HSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYIGS 481 ++Q+G VMVNLPTAG DYHVPFGGR SSYG REQG+ A++FYT+VKT+YI S Sbjct: 427 NAQSGCVMVNLPTAGTDYHVPFGGRGDSSYGPREQGQTARDFYTIVKTAYIAS 479 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: 589 Number of extensions: 18 Number of successful extensions: 2 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: 483 Length adjustment: 34 Effective length of query: 447 Effective length of database: 449 Effective search space: 200703 Effective search space used: 200703 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