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_012041851.1 BBTA_RS07435 succinate-semialdehyde dehydrogenase
Query= SwissProt::Q1JUP4 (481 letters) >NCBI__GCF_000015165.1:WP_012041851.1 Length = 479 Score = 330 bits (847), Expect = 5e-95 Identities = 185/470 (39%), Positives = 254/470 (54%), Gaps = 4/470 (0%) Query: 11 LLIDGEWVDAASGKTIDVVNPATGKPIGRVAHAGIADLDRALAAAQSGFEAWRKVPAHER 70 + IDG WV A G T DV++PATG+ I V AG AD+D A+ +A+ F+AW+ P ER Sbjct: 1 MFIDGRWVGALGGATFDVLDPATGETIDSVPEAGPADVDAAIRSAEMAFQAWKATPVAER 60 Query: 71 AATMRKAAALVRERADAIAQLMTQEQGKPLTEARVEVLSAADIIEWFADEGRRVYGRIVP 130 A + AA L+RE A+ + +L+T+E G+PL A E+ +A++++ +A+EG R++ + Sbjct: 61 ARLQKAAARLMRENAEQLGRLLTRELGRPLAGAITEIQRSAELLDVYAEEGLRLHAEMPL 120 Query: 131 PRNLGAQQTVVKEPVGPVAAFTPWNFPVNQVVRKLSAALATGCSFLVKAPEETPASPAAL 190 G + + +EP G V A TP+N+PV + KL AAL GC+ + K E+TP S L Sbjct: 121 TGVAGEKIIITREPAGVVIAITPFNYPVTLLCFKLGAALMAGCTVVAKPAEDTPLSTLRL 180 Query: 191 LRAFVDAGVPAGVIGLVYGDPAEISSYLIPHPVIRKVTFTGSTPVGKQLASLAGLHMKRA 250 F AG P G +V G ++ +I HP RK+ FTG T GK +A+ A MKR Sbjct: 181 AELFRKAGYPTGCFNVVTGRGPDVGMQMIAHPTPRKIAFTGGTQAGKAIAAAAAGTMKRV 240 Query: 251 TMELGGHAPVIVAEDADVALAVKAAGGAKFRNAGQVCISPTRFLVHNSIRDEFTRALVKH 310 T+ELGG P IV DAD+ A A F N+GQ C R V + F AL Sbjct: 241 TLELGGQCPAIVCADADIGAASAAIARHAFANSGQFCYRVNRVYVERPVYTRFLDALADR 300 Query: 311 AEGLKVGNGLEEGTTLGALANPRRLTAMASVIDNARKVGASIETGGERIG----SEGNFF 366 L VGNGL LG L N + I +AR GA+I TGG R+ +G F Sbjct: 301 VLQLDVGNGLTSTCALGPLVNEKIYRNSDRQIADARASGATILTGGARLTGGLYDKGWFL 360 Query: 367 APTVIANVPLDADVFNNEPFGPVAAIRGFDKLEEAIAEANRLPFGLAGYAFTRSFANVHL 426 PTVIA+ + + E FGPV + FD EA+ AN +GLA + F+R+ A Sbjct: 361 PPTVIADAGPSSLIMTEETFGPVLGVAPFDHHSEALRLANATIYGLAAFVFSRNLATGLT 420 Query: 427 LTQRLEVGMLWINQPATPWPEMPFGGVKDSGYGSEGGPEALEPYLVTKSV 476 L +RLE G +WIN PFGG+K SG G E G +E YL K++ Sbjct: 421 LAERLEAGSVWINDIQRSNQRAPFGGMKQSGIGREKGRYGVEDYLEYKTI 470 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: 632 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: 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 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