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 WP_011384974.1 AMB_RS13050 aldehyde dehydrogenase family protein
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_000009985.1:WP_011384974.1 Length = 479 Score = 265 bits (676), Expect = 3e-75 Identities = 165/477 (34%), Positives = 241/477 (50%), Gaps = 26/477 (5%) Query: 13 IDGEWVDAASG-KTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHERA 71 +DG WV A G + +DV+NPAT + GRVA G D RA+ AA F AW P ER Sbjct: 9 VDGAWVKPAKGSRLLDVINPATEQVSGRVALGGADDAVRAIQAAAKAFPAWAATPLAERL 68 Query: 72 ATMRKAAALVRERADAIAQLMTQEQGKPL------TEARVEV---LSAADIIEWFADEGR 122 + K A R D IA+ ++ E G PL +AR + +A + + +A E R Sbjct: 69 EILAKVTAGYERRLDEIAEAISLEMGAPLERLAKPAQARAGLGHFKTALSLAKTYAFERR 128 Query: 123 RVYGRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEE 182 + VVKEPVG V+ TPWN+P+NQ+ K++ ALA GC+ ++K E Sbjct: 129 Q------------GTTLVVKEPVGVVSLITPWNWPMNQIACKVAPALAAGCAMVLKPSEF 176 Query: 183 TPASPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASL 242 P S L +AGVPAGV +V+GD AEI L HP++ V+ TGS G + Sbjct: 177 APYSARILAEIIHEAGVPAGVFNMVFGDGAEIGPVLSSHPLVDMVSLTGSNLAGSSVMRE 236 Query: 243 AGLHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDE 302 +K+ ++ELGG + I+ + AD A+ A A N GQ C +P+R V DE Sbjct: 237 GAATIKKVSLELGGKSANIICDSADFKKAIGHAVKAMMGNTGQSCNAPSRLFVPAHRLDE 296 Query: 303 FTRALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIG-- 360 + +KVG+ + T +G +AN R+ + +I + GA + GG Sbjct: 297 AEGLAAELCAQIKVGDPSDPETVMGPIANGRQFDKVRRMIRTGMEEGAKLVCGGPERPEG 356 Query: 361 -SEGNFFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTR 419 +G F PTV + V + E FGPV ++RG+ L++A+A AN +GL+GY + Sbjct: 357 LDKGYFVRPTVFSRVTDAMTIMREEIFGPVLSMRGYADLDDAVAGANDCVYGLSGYVYAG 416 Query: 420 SFANVHLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSV 476 + +RL GM+ +N A P PFGG++ SG G E G E +L +K++ Sbjct: 417 DLDEARAVARRLRTGMVHLN-GALSHPGGPFGGIRQSGVGREWGEAGFEEFLESKTL 472 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: 645 Number of extensions: 32 Number of successful extensions: 4 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: 479 Length adjustment: 34 Effective length of query: 447 Effective length of database: 445 Effective search space: 198915 Effective search space used: 198915 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