Align Succinate-semialdehyde dehydrogenase [NADP(+)] 1; SSADH 1; SSDH 1; EC 1.2.1.79 (characterized)
to candidate N515DRAFT_4232 N515DRAFT_4232 L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate dehydrogenase
Query= SwissProt::P9WNX9 (457 letters) >FitnessBrowser__Dyella79:N515DRAFT_4232 Length = 1074 Score = 144 bits (362), Expect = 2e-38 Identities = 140/473 (29%), Positives = 189/473 (39%), Gaps = 29/473 (6%) Query: 3 IATINPATG-ETVKTFTAATDDEVDAAIARAHRRFADYRQTSFAQRARWANATADLLEAE 61 + NPA + V ++ +A V+ A+A A + + A RA A+ LEA Sbjct: 596 VQVTNPADRRQVVGSYVSADSATVEKALANAVAAQHGWDRLPAASRAAILEHAAEQLEAR 655 Query: 62 ADQAAAMMTLEMGKTLAAAKAEALKCAKGFRYYAENAEALLADEPADAAKVGASAAY--- 118 + A+ E GK L A AE + A RYYA A G S Sbjct: 656 RGEFIALCVREAGKGLPDAIAEIREAADFLRYYATMARRYFGQPEQLPGPTGESNQLFLN 715 Query: 119 GRYQPLGVILAVMPWNFPLWQAVRFAAPALMAGNVGLLKHASNVPQCALYLADVIARGGF 178 GR GV + + PWNFPL + A AL AGN + K A ++ G Sbjct: 716 GR----GVFVCISPWNFPLAIFLGQVAAALAAGNSVIAKPAEQTSLIGHAAVQLLHEAGV 771 Query: 179 PDGCFQTLLVSSGAVEAIL-RDPRVAAATLTGSEPAGQSVG---AIAGNEIKPTVLELGG 234 P Q L V A L RDPRVA TGS ++ A I + E GG Sbjct: 772 PADVLQYLPGDGATVGAALTRDPRVAGVAFTGSTETAWAINRALAARNAPIAALIAETGG 831 Query: 235 SDPFIVMPSADLDAAVSTAVTGRVQNNGQSCIAAKRFIVHADIYDDFVDKFVARMAALRV 294 + I SA + V AV+ Q+ GQ C AA+ V DI D MA L+V Sbjct: 832 QNAMIADSSALPEQIVKDAVSSAFQSAGQRCSAARVLYVQEDIADKVCAMLAGAMAELKV 891 Query: 295 GDPTDPDTDVGPLATEQGR----NEVAKQVEDAAAAGAVIRCGGKRLDRPGWFYPPTVIT 350 GDP TDVGP+ E R + A+ ++A G V G F+ P Sbjct: 892 GDPAQLSTDVGPVIDEDARKILVDHAARMDQEAKKIGEVAL--DPATTGNGTFFAPRAYE 949 Query: 351 DISKDMALYTEEVFGPVASVFR--AANIDEAVEIANATTFGLGSNAWTRDETEQRRFIDD 408 +A T E+FGPV V R + +D+ V+ NAT +GL +R + Sbjct: 950 --IPGLATLTREIFGPVLHVIRWKGSELDKVVDEINATGYGLTLGIHSRIDDTVEFIQSR 1007 Query: 409 IVAGQVFIN----GMTVSYPELPFGGVKRSGYGRELSA-HGIREFCNIKTVWI 456 G ++N G V PFGG SG G + H + F +T+ I Sbjct: 1008 ARVGNCYVNRNQIGAVVGVQ--PFGGEGLSGTGPKAGGPHYLFRFAGERTLTI 1058 Lambda K H 0.319 0.133 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: 880 Number of extensions: 45 Number of successful extensions: 5 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: 457 Length of database: 1074 Length adjustment: 39 Effective length of query: 418 Effective length of database: 1035 Effective search space: 432630 Effective search space used: 432630 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 54 (25.4 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