Align Putative succinate-semialdehyde dehydrogenase [NADP(+)] 2; SSADH 2; SSDH 2; EC 1.2.1.79 (characterized)
to candidate WP_110206407.1 DNK54_RS08025 succinate-semialdehyde dehydrogenase (NADP(+))
Query= SwissProt::P9WNX7 (518 letters) >NCBI__GCF_003194585.1:WP_110206407.1 Length = 538 Score = 437 bits (1125), Expect = e-127 Identities = 230/483 (47%), Positives = 308/483 (63%), Gaps = 1/483 (0%) Query: 35 GKPLTTIPVGTAADVEAAFAEARAAQTDWAKRPVIERAAVIRRYRDLVIENREFLMDLLQ 94 G+PL IP + DV AAF AR AQ W++ + RA ++ R LV++ E + D+ Sbjct: 56 GQPLAVIPQSSDDDVRAAFERARRAQAAWSRTSLDHRAEIMLRLHKLVLDRAEEICDVAV 115 Query: 95 AEAGKARWAAQEEIVDLIANANYYARVCVDLLKPRKAQPLLPGIGKTTVCYQPKGVVGVI 154 E+GKAR A E + A YYAR + ++ ++P + V PKGVVG+I Sbjct: 116 WESGKARKDAYLEAYHVALTARYYARTIHRHMDSQRRPGVVPLATRIDVNRVPKGVVGII 175 Query: 155 SPWNYPMTLTVSDSVPALVAGNAVVLKPDSQTPYCALACAELLYRAGLPRALYAIVPGPG 214 SPWNYP T+ + D +PAL+AGNAVV KPDSQT AL A+LL AG P+ L+ +V GPG Sbjct: 176 SPWNYPFTMALCDGLPALMAGNAVVAKPDSQTMLTALLGAQLLEEAGFPKDLWTVVAGPG 235 Query: 215 SVVGTAITDNCDYLMFTGSSATGSRLAEHAGRRLIGFSAELGGKNPMIVARGANLDKVAK 274 S VGT I +N DY+ FTGS+ATG R+A RLIG S ELGGKNP+++ R A+++ A+ Sbjct: 236 SRVGTRIIENADYVCFTGSTATGKRVAAGCAERLIGCSLELGGKNPILILRDADIETAAE 295 Query: 275 AATRACFSNAGQLCISIERIYVEKDIAEEFTRKFGDAVRNMKLGTAYDFSVDMGSLISEA 334 ATRA FSNAGQLC+S ER+ V +I + F +F M LG +++ DMGSLIS+ Sbjct: 296 GATRATFSNAGQLCVSTERMMVADEIYDRFVERFVARTEAMVLGPGHNWETDMGSLISQD 355 Query: 335 QLKTVSGHVDDATAKGAKVIAGGKARPDIGPLFYEPTVLTNVAPEMECAANETFGPVVSI 394 QL TV HV DA AKGAKV+ GGK RPD+GP F+EPT+L V EM C NETFGPV+S+ Sbjct: 356 QLDTVKAHVADAVAKGAKVLTGGKHRPDLGPFFFEPTILEGVTEEMTCFGNETFGPVISL 415 Query: 395 YPVADVDEAVEKANDTDYGLNASVWAGSTAEGQRIAARLRSGTVNVDEGYAFAWGSLSAP 454 Y D +A+ KAN+ +YGLNAS+++ + IA ++ GTVN++EGY + SL AP Sbjct: 416 YRFHDETKAIAKANEGNYGLNASIYSRDGKRARAIAREIKCGTVNINEGYGATFASLDAP 475 Query: 455 MGGMGLSGVGRRHGPEGLLKYTESQTIATARVFNLDPPFGIPATVWQKSLLPIVRTVMKL 514 MGGM SG+GRR G EG+ +YTE+Q + T R + P G+ + K +L + +MK Sbjct: 476 MGGMRESGMGRRQGAEGIHRYTETQAVGTQRGWGFRPVPGMSNETFAK-VLTLNERLMKK 534 Query: 515 PGR 517 GR Sbjct: 535 LGR 537 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: 659 Number of extensions: 24 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: 518 Length of database: 538 Length adjustment: 35 Effective length of query: 483 Effective length of database: 503 Effective search space: 242949 Effective search space used: 242949 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