Align 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_013093960.1 BC1002_RS31175 aldehyde dehydrogenase family protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_1109 (481 letters) >NCBI__GCF_000092885.1:WP_013093960.1 Length = 480 Score = 642 bits (1655), Expect = 0.0 Identities = 321/474 (67%), Positives = 371/474 (78%), Gaps = 1/474 (0%) Query: 6 RYDNYINGEWVSGADYSANINPSELTDTIGDYAKADLAQVHAAIDAARAAFPAWSTSGIQ 65 ++ NYI+G+WV GA S N+NPS L D IG++A+AD Q H AI AAR AF WS S Q Sbjct: 3 QFANYIDGQWVDGASVSRNVNPSNLDDVIGEFAQADAEQTHRAISAARKAFATWSLSTPQ 62 Query: 66 ARHDSLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDY 125 R D LD+ G+ ILAR+ ELG LLAREEGKTLPEAIGEV RAG IFKFFAGE LR+ G+ Sbjct: 63 QRFDVLDQAGSAILARKAELGKLLAREEGKTLPEAIGEVGRAGQIFKFFAGEALRVGGEI 122 Query: 126 LPSVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLVPGCAW 185 +PSVRPG+ VE+TRE +GVVGLITPWNFPIAIPAWKIAPALAYGN VV+KPADLVPG W Sbjct: 123 VPSVRPGMTVEMTREPVGVVGLITPWNFPIAIPAWKIAPALAYGNTVVIKPADLVPGSTW 182 Query: 186 ALAEIISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQIAVSCVSRQA 245 L +II+ AG PAGV NLVMG G VVG+ALV SP VD ISFTGSV GR I C Sbjct: 183 ELVKIIAEAGAPAGVINLVMGRGSVVGEALVSSPHVDAISFTGSVSTGRAIGAKCFESGK 242 Query: 246 KVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGIHDKFVEAMA 305 K QLEMGGKNP ++LDDADL A+E + AFYSTGQRCTASSR IVTAGI+D+F++ M Sbjct: 243 KFQLEMGGKNPMVVLDDADLDVAIEACINGAFYSTGQRCTASSRLIVTAGIYDRFIDGMK 302 Query: 306 ERMKSIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGGLVACDTEGYFL 365 RM+++KVG AL GT IGPVV QLEQD +Y+ I + EG V GG V T G FL Sbjct: 303 ARMRALKVGDALADGTQIGPVVDDKQLEQDERYLAIAREEGG-TVFGGERVQGVTPGNFL 361 Query: 366 APTLFADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSAGIATTSLKYANH 425 AP L ++T+AMRI+REE+FGPVA++++V DY+ ALA+ANDTEFGLSAGI TTSLKYA+H Sbjct: 362 APALVTETTSAMRINREEVFGPVASVIKVKDYQEALAVANDTEFGLSAGICTTSLKYASH 421 Query: 426 FKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGSREQGRYAQEFYTVVKTSYI 479 F+RH QAGMVMVN TAGVDYHVPFGGRKGSSYG REQG YA+EFYT VKT+YI Sbjct: 422 FRRHVQAGMVMVNTATAGVDYHVPFGGRKGSSYGPREQGAYAREFYTSVKTAYI 475 Lambda K H 0.318 0.134 0.391 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: 695 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: 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 24 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