Align Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized)
to candidate HSERO_RS19695 HSERO_RS19695 aldehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__HerbieS:HSERO_RS19695 Length = 480 Score = 449 bits (1154), Expect = e-130 Identities = 225/472 (47%), Positives = 313/472 (66%) Query: 6 YTDTQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKV 65 Y D QL IDG + + +V +PATG +GR+ A AD++ A+ AA F+ WR+V Sbjct: 2 YPDLQLYIDGRFHGVEGRRYQEVRDPATGDVLGRLPWAERADIEEAIQAAHRAFQQWRQV 61 Query: 66 PAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVY 125 ER+ +R+AAAL RERA A+A +T + GKPL +A E+++AA+ ++W A+EGRR+Y Sbjct: 62 SPLERSDILRRAAALARERAQAMAPAITMDNGKPLADAVAEIINAAEHLDWHAEEGRRLY 121 Query: 126 GRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPA 185 GR+V R+ +Q VV+EPVG AA +PWNFP Q ++K++AA+A GC+ ++K P E+PA Sbjct: 122 GRVVGARHPEVRQLVVREPVGVCAAISPWNFPFGQAMKKVAAAMAAGCTVVLKGPSESPA 181 Query: 186 SPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGL 245 + + + F DAGVPAGV +V G +EIS +LI P++R ++FTGS PVG +LA+ A L Sbjct: 182 AIVLMAQLFHDAGVPAGVFNIVSGVSSEISQHLIESPLVRNISFTGSVPVGSKLAAQAAL 241 Query: 246 HMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTR 305 HMKR +MELGGHAPV+V +DA+V A + K RNAGQVC+SP+RF V I F Sbjct: 242 HMKRMSMELGGHAPVLVFDDAEVEPAARLLARLKTRNAGQVCVSPSRFYVQKGIYARFVT 301 Query: 306 ALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNF 365 A + +KVG G E G +G L + RR A+ +ID+A G+ + TGG R+G G+F Sbjct: 302 AFAEALLQIKVGPGHEPGVQMGPLIHGRRFEAVQGLIDDALAQGSELVTGGARLGQRGHF 361 Query: 366 FAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVH 425 +APT+I VP A V EPFGP+AA+ F + EEAIA AN LP GLA Y FT+S H Sbjct: 362 YAPTLITGVPPSARVMQEEPFGPIAAVTPFSQAEEAIAMANALPLGLASYVFTQSLDTAH 421 Query: 426 LLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVT 477 +++ L+ GM+ IN PE+PFGG+ +SG+GSEGG E E +LVTK ++ Sbjct: 422 RVSRDLQAGMVNINHSGMAHPELPFGGIGESGFGSEGGVEGFESFLVTKMIS 473 Lambda K H 0.318 0.134 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: 688 Number of extensions: 31 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