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_RS07235 HSERO_RS07235 aldehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__HerbieS:HSERO_RS07235 Length = 477 Score = 626 bits (1614), Expect = 0.0 Identities = 310/476 (65%), Positives = 369/476 (77%) Query: 6 YTDTQLLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKV 65 Y D QL I+GEW +ASG+TIDV+NPAT + IG++AHA ADLDRAL AA GFE WR + Sbjct: 2 YKDVQLFINGEWTASASGRTIDVINPATEEVIGKIAHADRADLDRALEAASKGFETWRNM 61 Query: 66 PAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVY 125 A ER+ MR+AA L+RERA+ +A+LMT EQGKPL EA++E L AAD I+WFA+E RR Y Sbjct: 62 SAFERSKIMRRAADLLRERAEEVARLMTMEQGKPLAEAKMETLGAADTIDWFAEEARRTY 121 Query: 126 GRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPA 185 GR+VP R GA Q V+KEPVGPVAAFTPWNFP+NQVVRKLSAALA GCS +VKAPEETPA Sbjct: 122 GRLVPARVPGAYQMVIKEPVGPVAAFTPWNFPLNQVVRKLSAALAAGCSIIVKAPEETPA 181 Query: 186 SPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGL 245 SPA L+RA+ DAGVPAGVI LVYG PAEIS YLIPHPVI+K++FTGSTPVGKQLA+LAG Sbjct: 182 SPAELIRAYADAGVPAGVINLVYGVPAEISEYLIPHPVIKKISFTGSTPVGKQLAALAGQ 241 Query: 246 HMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTR 305 HMKRATMELGGHAP +V +DADV +A K AKFRNAGQVC+SPTRFLV + + F Sbjct: 242 HMKRATMELGGHAPAMVFDDADVDVAAKMLATAKFRNAGQVCVSPTRFLVQKGVFNAFVD 301 Query: 306 ALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGNF 365 V +AE LKVGNGLE G T+G +AN RR+ A+ ++ID+A GA + TGG+RIG++G F Sbjct: 302 KFVTYAEQLKVGNGLEAGITMGPVANKRRIPALEALIDDAVSQGAQLRTGGKRIGNKGYF 361 Query: 366 FAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVH 425 F PTV+ N+PL A N EPFGP+A I F+ L+E I EANRLP+GLA YAF +S H Sbjct: 362 FQPTVLTNLPLQARAMNEEPFGPLALINSFETLDEVITEANRLPYGLAAYAFAKSAHTKH 421 Query: 426 LLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVTVMAV 481 L R+E GML IN PE+PFGG+KDSGYGSEGG EA+E Y+ TK VT + V Sbjct: 422 ALAARVESGMLTINHLGLALPELPFGGIKDSGYGSEGGTEAIEAYINTKLVTQLDV 477 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: 764 Number of extensions: 32 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: 477 Length adjustment: 34 Effective length of query: 447 Effective length of database: 443 Effective search space: 198021 Effective search space used: 198021 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