Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate BPHYT_RS28770 BPHYT_RS28770 aldehyde dehydrogenase
Query= reanno::WCS417:GFF827 (481 letters) >FitnessBrowser__BFirm:BPHYT_RS28770 Length = 480 Score = 632 bits (1631), Expect = 0.0 Identities = 312/474 (65%), Positives = 375/474 (79%), Gaps = 1/474 (0%) Query: 6 RFDNYINGQWVAGADYCVNLNPSELSDVIGEYAKADVTQVNAAIDAARAAFPAWSTSGIQ 65 +F N++ G+WV G D+ N+NPS+ SDVIG +A+A Q AI +AR+AF WS S Q Sbjct: 3 QFKNFVGGEWVDGNDFAPNVNPSDTSDVIGHFARASADQTQKAIASARSAFRTWSLSTPQ 62 Query: 66 ARHDALDKVGSEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDY 125 R D LD+ GS ILAR+ ELG LLAREEGKTL EA+GEV RAG IFKFFAGE LR+ G+ Sbjct: 63 QRFDLLDQAGSTILARKNELGKLLAREEGKTLAEAVGEVGRAGQIFKFFAGEALRVGGEI 122 Query: 126 VPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGCAW 185 +PSVRPG+ VEVTRE +GV+GLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPG W Sbjct: 123 LPSVRPGLTVEVTREPVGVIGLITPWNFPIAIPAWKIAPALAYGNCVVIKPAELVPGSVW 182 Query: 186 ALAEIISRAGFPAGVFNLVMGSGRVVGDVLVNSPKVDGISFTGSVGVGRQIAVSCVSRQA 245 L +II+ AG PAGV NLVMG G +VG++LV S VD +SFTGSVG G+ IA CV+ Sbjct: 183 ELVKIIAEAGAPAGVINLVMGMGSIVGEILVMSADVDAVSFTGSVGTGQAIAAKCVATGK 242 Query: 246 KVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRLIVTAGIHDQFVAAMA 305 K QLEMGGKNP ++LDDADL AVE + AFYSTGQRCTASSRLIVT+GIHD+FV AM Sbjct: 243 KFQLEMGGKNPMVVLDDADLDVAVEACINGAFYSTGQRCTASSRLIVTSGIHDRFVEAML 302 Query: 306 ERMKSIKVGHALKSGTDIGPVVSQAQLDQDLKYIDIGQSEGARLVSGGGLVTCDTEGYYL 365 RM+S+K+G+AL + T IGPVV QL+QD +YI++ ++EG V GG VT TEG++L Sbjct: 303 ARMRSLKIGNALDASTQIGPVVDAKQLEQDERYIELARNEGGS-VFGGERVTSATEGFFL 361 Query: 366 APTLFADSEAAMRISREEIFGPVANVVRVADYEAALAMANDTEFGLSAGIATTSLKYANH 425 AP L ++ AM I+REE+FGPVA+V++VA+YE ALA+AND+ FGLSAGI T SL +A+H Sbjct: 362 APALVTNTTPAMTINREEVFGPVASVIKVANYEEALAVANDSPFGLSAGICTMSLAHASH 421 Query: 426 FKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYI 479 FKRH QAGMVM+N TAGVDYHVPFGGRKGSS G REQG YA+EFYT+VKT+Y+ Sbjct: 422 FKRHVQAGMVMINTATAGVDYHVPFGGRKGSSLGPREQGTYAREFYTIVKTAYV 475 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: 667 Number of extensions: 15 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: 480 Length adjustment: 34 Effective length of query: 447 Effective length of database: 446 Effective search space: 199362 Effective search space used: 199362 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: 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