Align succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized)
to candidate WP_082697952.1 AQZ52_RS13580 NAD-dependent succinate-semialdehyde dehydrogenase
Query= reanno::MR1:200453 (482 letters) >NCBI__GCF_001519075.1:WP_082697952.1 Length = 475 Score = 551 bits (1421), Expect = e-161 Identities = 279/454 (61%), Positives = 336/454 (74%), Gaps = 1/454 (0%) Query: 28 VAITNPATGAVIACVPVMGQAETQAAIAAAEAALPAWRALTAKERGAKLRRWFELLNENS 87 +A+ NPATGA+IA V AE A I AA+AA PAW A TAK R A LRRW+ L+ E Sbjct: 17 LAVHNPATGALIATVRDYAPAEIAAIIDAADAARPAWAAETAKARAAVLRRWYALIMERQ 76 Query: 88 DDLALLMTSEQGKPLTEAKGEVTYAASFIEWFAEEAKRIYGDTIPGHQGDKRIMVIKQPV 147 ++LA L+T+E GKPL EA+GEV Y ASFIEWFAEEAKR YG+T+P KR++ IKQPV Sbjct: 77 EELAALITAECGKPLAEARGEVAYGASFIEWFAEEAKRAYGETVPTFAVGKRVLTIKQPV 136 Query: 148 GVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPAPQTPFTALALAVLAERAGIPAGVFS 207 G AAITPWNFP AMITRK PALAAGC++VVKPA TP +ALAL LA AG+PA +F Sbjct: 137 GTCAAITPWNFPIAMITRKVGPALAAGCSIVVKPAEATPLSALALETLAREAGVPADLFR 196 Query: 208 VI-TGDAIAIGNEMCTNPIVRKLSFTGSTNVGIKLMAQCAPTLKKLSLELGGNAPFIVFD 266 V + D +G C +P VRKLSFTGST VG LMAQ A + +LSLELGGNAPFIVFD Sbjct: 197 VTPSNDPAGVGALFCHHPKVRKLSFTGSTRVGKILMAQAAENVTRLSLELGGNAPFIVFD 256 Query: 267 DANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVYDEFAEKLSMAVAKLKVGEGIIAGV 326 DA++DAA +G M +K+RNAGQTCVCANR+ VQ V+D F E+L VA L VG+G G Sbjct: 257 DADLDAAADGLMASKFRNAGQTCVCANRVLVQDSVHDAFVERLRAKVAALVVGDGAAPGT 316 Query: 327 TTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKVHELGGNFFEPTVLTNADKSMRVAREE 386 T GPLINAAAVEKV+S + DA+ GAT L GG ++G +FFEPTVL + M +A E Sbjct: 317 TIGPLINAAAVEKVESLVGDALAGGATALMGGHRSDVGASFFEPTVLAGVNPQMAIATSE 376 Query: 387 TFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYGRDISLVWKVAESLEYGMVGVNTGLIS 446 FGP+ PL +F D D ++ ANDT FGLAAYF+ RD+ VW+V E+LEYGMVGVN G+IS Sbjct: 377 IFGPVVPLIRFKDEDQAVRIANDTPFGLAAYFFARDLGRVWRVMEALEYGMVGVNDGIIS 436 Query: 447 TEVAPFGGMKSSGLGREGSKYGIEEYLEIKYICM 480 TEVAPFGG+K SGLGREGS++G++EYLE+KY M Sbjct: 437 TEVAPFGGIKQSGLGREGSRHGLDEYLELKYCLM 470 Lambda K H 0.318 0.133 0.390 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: 634 Number of extensions: 22 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: 482 Length of database: 475 Length adjustment: 34 Effective length of query: 448 Effective length of database: 441 Effective search space: 197568 Effective search space used: 197568 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