Align succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized)
to candidate 3609503 Dshi_2887 succinic semialdehyde dehydrogenase (RefSeq)
Query= reanno::MR1:200453 (482 letters) >FitnessBrowser__Dino:3609503 Length = 492 Score = 646 bits (1666), Expect = 0.0 Identities = 320/481 (66%), Positives = 381/481 (79%), Gaps = 1/481 (0%) Query: 3 LNDPSLLRQQCYINGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAALP 62 L DP+LL + Y G W DA+S T +TNPA G VIA VP +G+AET AIAAA+AA Sbjct: 12 LKDPALLASKAYFAGAWTDADSGATFPVTNPARGDVIAHVPDLGRAETARAIAAADAAQK 71 Query: 63 AWRALTAKERGAKLRRWFELLNENSDDLALLMTSEQGKPLTEAKGEVTYAASFIEWFAEE 122 W A TAK+R LRRWF+L+ N+DDLA ++T+E GKPL EA+GEV Y ASF+EWFAEE Sbjct: 72 PWAARTAKDRAQVLRRWFDLIVGNADDLARILTAEMGKPLAEARGEVMYGASFVEWFAEE 131 Query: 123 AKRIYGDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPA 182 AKR+YG+TIPGH D RI VI+QP+GV AITPWNFP AMITRKAAPALAAGC + KPA Sbjct: 132 AKRLYGETIPGHLPDARIQVIRQPIGVVGAITPWNFPIAMITRKAAPALAAGCAFLSKPA 191 Query: 183 PQTPFTALALAVLAERAGIPAGVFSVI-TGDAIAIGNEMCTNPIVRKLSFTGSTNVGIKL 241 TP +ALALAVLAERAGIPAG+F+V+ + D+ AIG E C N VRKL+FTGST VG L Sbjct: 192 EDTPLSALALAVLAERAGIPAGLFAVLPSSDSSAIGKEFCENHTVRKLTFTGSTQVGRIL 251 Query: 242 MAQCAPTLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGV 301 +AQ A +KK S+ELGGNAPFIVFDDA++D AVEGAM K+RNAGQTCVCANRIYVQ GV Sbjct: 252 LAQAADQVKKCSMELGGNAPFIVFDDADLDKAVEGAMACKFRNAGQTCVCANRIYVQDGV 311 Query: 302 YDEFAEKLSMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKVH 361 YD FAEKL+ AV +LKVG+G GVT GPLIN AVEKVQ HL+D KG TV+ GG+ H Sbjct: 312 YDAFAEKLAAAVEELKVGDGAAEGVTIGPLINMPAVEKVQDHLDDLRAKGGTVVTGGETH 371 Query: 362 ELGGNFFEPTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYGR 421 LGG FF PTV+T + M+VAREETFGP+APLF+F + D+VI ANDT FGLA YFY R Sbjct: 372 PLGGTFFTPTVVTGVTQEMKVAREETFGPVAPLFRFTEEDEVIAMANDTIFGLAGYFYAR 431 Query: 422 DISLVWKVAESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIKYICMS 481 DI + +V+E+LEYG+VG+NTG+ISTE APFGG+K SGLGREGS++GI+EYLE+KYIC+S Sbjct: 432 DIGRITRVSEALEYGIVGINTGIISTEGAPFGGVKQSGLGREGSRHGIDEYLEMKYICLS 491 Query: 482 V 482 + Sbjct: 492 I 492 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: 699 Number of extensions: 18 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: 492 Length adjustment: 34 Effective length of query: 448 Effective length of database: 458 Effective search space: 205184 Effective search space used: 205184 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 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