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 RR42_RS29720 RR42_RS29720 aldehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >FitnessBrowser__Cup4G11:RR42_RS29720 Length = 476 Score = 482 bits (1240), Expect = e-140 Identities = 241/473 (50%), Positives = 325/473 (68%), Gaps = 1/473 (0%) Query: 6 YTDTQLLIDGEWVDAASG-KTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRK 64 Y + L I+GE++ K+ DV NPAT + +GR+ HA IADL A+A +QS F WRK Sbjct: 2 YPELFLYINGEFIGVGGQRKSEDVTNPATREVLGRLPHATIADLAHAVATSQSAFLKWRK 61 Query: 65 VPAHERAATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRV 124 +R+ +R+AA+L RERAD IAQ +T +QGKPL EAR EV++ AD +W A+E RR+ Sbjct: 62 SSPLQRSEILRRAASLARERADDIAQAITLDQGKPLAEARAEVVTCADHADWHAEECRRI 121 Query: 125 YGRIVPPRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETP 184 YGR++PPR+ +Q VV+EPVG AFTPWNFP NQ +RK++AA+ GC+ ++K PE++P Sbjct: 122 YGRVIPPRDTAVRQIVVREPVGVCVAFTPWNFPFNQAIRKITAAIGAGCAIVLKGPEDSP 181 Query: 185 ASPAALLRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAG 244 ++ AL + F DAG+P GV+ +V+G P E+S +LI HP++RKV+FTGS VGK+LA+LAG Sbjct: 182 SAIVALAKLFHDAGLPPGVLNIVWGVPHEVSDFLIQHPLVRKVSFTGSVDVGKKLAALAG 241 Query: 245 LHMKRATMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFT 304 HMKRATMELGGHAPVIV +DADV AV+ K RNAGQVC++PTR V + I +F Sbjct: 242 HHMKRATMELGGHAPVIVCDDADVDSAVQVTMRMKLRNAGQVCVAPTRLFVQSGIYTKFR 301 Query: 305 RALVKHAEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIGSEGN 364 +++ E ++G G++ TT+G LA+ RR+ M + +A+ G ++ TGG G+ Sbjct: 302 DQMIEAFETARLGPGIDSSTTMGPLAHARRVKEMERFVADAKARGGNVLTGGFAPELGGS 361 Query: 365 FFAPTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANV 424 FFAPT++ N+ AD+ EPFGP+A + FD L+EAIA AN LPFGLA +AFT + Sbjct: 362 FFAPTLVDNLDDTADLMQKEPFGPIAPLAKFDTLDEAIARANSLPFGLAAFAFTERTRSA 421 Query: 425 HLLTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSVT 477 H L LE GM+ IN PE PFGG+KDSG GSEGG E + YL TK VT Sbjct: 422 HRLATELEAGMVNINHAGMALPETPFGGIKDSGMGSEGGTETFDGYLTTKFVT 474 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: 640 Number of extensions: 24 Number of successful extensions: 1 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: 476 Length adjustment: 34 Effective length of query: 447 Effective length of database: 442 Effective search space: 197574 Effective search space used: 197574 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