Align succinate-semialdehyde dehydrogenase (NADP+) [EC: 1.2.1.16] (characterized)
to candidate 3608018 Dshi_1425 aldehyde dehydrogenase (RefSeq)
Query= reanno::MR1:200453 (482 letters) >FitnessBrowser__Dino:3608018 Length = 484 Score = 305 bits (781), Expect = 2e-87 Identities = 183/467 (39%), Positives = 255/467 (54%), Gaps = 16/467 (3%) Query: 15 INGQWCDANSKETVAITNPATGAVIACVPVMGQAETQAAIAAAEAALPAWRALTAKERGA 74 ING D S + + NPAT V+A P + + + AIAAA+AA P W AL+ ERGA Sbjct: 23 INGALVD--SAGSFEVFNPATDEVVAHAPNASRDQVEQAIAAAKAAQPGWAALSQDERGA 80 Query: 75 KLRRWFELLNENSDDLALLMTSEQGKPL-TEAKGEVTYAASFIEWFAEEAKRIYGDTIPG 133 + + + L+ + +L L+T+EQGKP + A EV YA I W E AKR D + Sbjct: 81 YIAAYADALDAHKQELITLLTTEQGKPRHSMATTEVEYA---IFWVREVAKRRLEDEVIE 137 Query: 134 HQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPAPQTPFTALALA 193 + + V P+GV AITPWNFP + K AP L G TMV+KP+P TP L Sbjct: 138 DTPEHTVKVAHTPLGVVGAITPWNFPVLLGLWKIAPCLVTGNTMVMKPSPYTPLCTLRFG 197 Query: 194 VLAERAGIPAGVFSVITGDAIAIGNE----MCTNPIVRKLSFTGSTNVGIKLMAQCAPTL 249 +A++ PAGV +V+ G GNE + +P + K+SFTGST G K+MA + L Sbjct: 198 EIAQQV-FPAGVLNVVAG-----GNEQGAWLTEHPDIAKISFTGSTATGRKVMASSSCNL 251 Query: 250 KKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVYDEFAEKL 309 K+++LELGGN P I+ + + A Y N+GQ C+ R+YV +YD+F Sbjct: 252 KRITLELGGNDPAILLPGTDYKPLIPTLFDAAYGNSGQWCIAVKRLYVHESLYDDFLRDF 311 Query: 310 SMAVAKLKVGEGIIAGVTTGPLINAAAVEKVQSHLEDAIKKGATVLAGGKVHELGGNFFE 369 A+ VG G+ GP+ N K++ D +G +V GG++ + GNF Sbjct: 312 VAHAAEKTVGNGMDPNTDLGPIQNKMQYGKLKDLFADVKAQGLSVPLGGEIPDGPGNFVP 371 Query: 370 PTVLTNADKSMRVAREETFGPLAPLFKFNDVDDVIKQANDTEFGLAAYFYGRDISLVWKV 429 T++ N K RV REE FGP+ P+ K++D+D+V++ ANDTEFGLAA +G D V Sbjct: 372 ITIVDNPPKDSRVVREEPFGPILPIIKWSDLDEVVRDANDTEFGLAASVWGPDRDTAIGV 431 Query: 430 AESLEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIEEYLEIK 476 A LE G V VN I PFGG K SG+G E + G++E+ K Sbjct: 432 ANRLEAGTVWVNEIHIHGIDIPFGGHKQSGMGVENGQEGLKEFTNTK 478 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: 575 Number of extensions: 29 Number of successful extensions: 3 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: 484 Length adjustment: 34 Effective length of query: 448 Effective length of database: 450 Effective search space: 201600 Effective search space used: 201600 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