Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate 3608018 Dshi_1425 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::Q88RC0 (480 letters) >FitnessBrowser__Dino:3608018 Length = 484 Score = 294 bits (752), Expect = 5e-84 Identities = 173/463 (37%), Positives = 253/463 (54%), Gaps = 10/463 (2%) Query: 15 INGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTAKERSA 74 ING +D+ + +V NPAT EV+ P + +AI AA A P W AL+ ER A Sbjct: 23 INGALVDSAG--SFEVFNPATDEVVAHAPNASRDQVEQAIAAAKAAQPGWAALSQDERGA 80 Query: 75 KLRRWFELMIENQDDLARLMTTEQGKPL-AEAKGEIAYAASFIEWFAEEAKRIYGDTIPG 133 + + + + ++ +L L+TTEQGKP + A E+ YA I W E AKR D + Sbjct: 81 YIAAYADALDAHKQELITLLTTEQGKPRHSMATTEVEYA---IFWVREVAKRRLEDEVIE 137 Query: 134 HQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPASQTPYSALALV 193 P+ + V P+GV AITPWNFP + K P L G TMV+KP+ TP L Sbjct: 138 DTPEHTVKVAHTPLGVVGAITPWNFPVLLGLWKIAPCLVTGNTMVMKPSPYTPLCTLRFG 197 Query: 194 ELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQLMEECAKDIKKVS 253 E+A + PAGVL+VV G E G LT + + K+SFTGST GR++M + ++K+++ Sbjct: 198 EIAQQV-FPAGVLNVVAGG-NEQGAWLTEHPDIAKISFTGSTATGRKVMASSSCNLKRIT 255 Query: 254 LELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGVYDAFAEKLAAAV 313 LELGGN P I+ D + + Y N+GQ C+ R+YV + +YD F A Sbjct: 256 LELGGNDPAILLPGTDYKPLIPTLFDAAYGNSGQWCIAVKRLYVHESLYDDFLRDFVAHA 315 Query: 314 AKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLIE--GNFFEPTIL 371 A+ +GNG++ T GP+ + K+++ D ++G V GG++ + GNF TI+ Sbjct: 316 AEKTVGNGMDPNTDLGPIQNKMQYGKLKDLFADVKAQGLSVPLGGEIPDGPGNFVPITIV 375 Query: 372 VDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYARDMSRVFRVAEAL 431 + PK + V +EE FGP+ P+ ++ D EV+ +NDTEFGLA+ + D VA L Sbjct: 376 DNPPKDSRVVREEPFGPILPIIKWSDLDEVVRDANDTEFGLAASVWGPDRDTAIGVANRL 435 Query: 432 EYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIK 474 E G V +N I PFGG K SG+G E + G++++ K Sbjct: 436 EAGTVWVNEIHIHGIDIPFGGHKQSGMGVENGQEGLKEFTNTK 478 Lambda K H 0.317 0.134 0.384 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: 598 Number of extensions: 29 Number of successful extensions: 4 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: 480 Length of database: 484 Length adjustment: 34 Effective length of query: 446 Effective length of database: 450 Effective search space: 200700 Effective search space used: 200700 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 (21.6 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