Align Putative succinate-semialdehyde dehydrogenase [NADP(+)] 2; SSADH 2; SSDH 2; EC 1.2.1.79 (characterized)
to candidate WP_110208380.1 DNK54_RS17710 succinate-semialdehyde dehydrogenase (NADP(+))
Query= SwissProt::P9WNX7 (518 letters) >NCBI__GCF_003194585.1:WP_110208380.1 Length = 522 Score = 420 bits (1079), Expect = e-122 Identities = 214/456 (46%), Positives = 284/456 (62%) Query: 26 TRTIDEVFTGKPLTTIPVGTAADVEAAFAEARAAQTDWAKRPVIERAAVIRRYRDLVIEN 85 T + EV+TG L +P + D+EAAFA AR AQ WA P+ +R V +++ LV+E Sbjct: 31 TWKLTEVYTGDVLVELPQSSPEDIEAAFAAARRAQKAWAATPLKQRLKVFKKFHSLVLER 90 Query: 86 REFLMDLLQAEAGKARWAAQEEIVDLIANANYYARVCVDLLKPRKAQPLLPGIGKTTVCY 145 E ++DL+Q E+GKAR A EE +D+ YY + +L RK +P + + Sbjct: 91 NETIVDLIQVESGKARRMAFEETLDVPMVTGYYLKRAAKVLATRKHAGPVPVVSSSQEVR 150 Query: 146 QPKGVVGVISPWNYPMTLTVSDSVPALVAGNAVVLKPDSQTPYCALACAELLYRAGLPRA 205 PKGVVG+I+PWN+P +SD++PAL+AGN VV+KPD++T L +LL AGLP+ Sbjct: 151 IPKGVVGIIAPWNFPFATGISDAIPALIAGNGVVVKPDNKTALSPLFGVQLLEEAGLPKG 210 Query: 206 LYAIVPGPGSVVGTAITDNCDYLMFTGSSATGSRLAEHAGRRLIGFSAELGGKNPMIVAR 265 L+ +V G G VG + DN +Y+MFTGS+ TG + E AGR LIG ELGGKNPMIV Sbjct: 211 LFQVVCGEGPDVGPTLIDNANYVMFTGSTNTGRVIGERAGRNLIGACLELGGKNPMIVLP 270 Query: 266 GANLDKVAKAATRACFSNAGQLCISIERIYVEKDIAEEFTRKFGDAVRNMKLGTAYDFSV 325 ANLD V K A F N GQ+C+ IER+YV I + F +F +A + +G AYDF Sbjct: 271 DANLDDVVKGALFGAFGNTGQICMHIERMYVHDSIYDTFKARFKEATEKLVVGAAYDFGP 330 Query: 326 DMGSLISEAQLKTVSGHVDDATAKGAKVIAGGKARPDIGPLFYEPTVLTNVAPEMECAAN 385 ++GSLIS V+ HV DA KGA V+ GGK RPD+GP F+EPT+L V EM Sbjct: 331 NVGSLISVEHKDRVASHVADALEKGATVVTGGKERPDLGPAFFEPTILEGVTEEMLAGVT 390 Query: 386 ETFGPVVSIYPVADVDEAVEKANDTDYGLNASVWAGSTAEGQRIAARLRSGTVNVDEGYA 445 ETFGPVV+++ DEA+ AN TDYGLNASVW G R+ R+ SG VN+++ A Sbjct: 391 ETFGPVVALHRYQTEDEAISLANATDYGLNASVWGGDLDNAIRVGKRIESGNVNINDILA 450 Query: 446 FAWGSLSAPMGGMGLSGVGRRHGPEGLLKYTESQTI 481 A+ S P GG+ SGVG RHG +GLLKYT+ Q + Sbjct: 451 TAYASKGTPSGGVKQSGVGARHGDQGLLKYTDCQNV 486 Lambda K H 0.318 0.134 0.396 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: 694 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: 518 Length of database: 522 Length adjustment: 35 Effective length of query: 483 Effective length of database: 487 Effective search space: 235221 Effective search space used: 235221 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: 52 (24.6 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