Align Putative aldehyde dehydrogenase FUS7; Fusarin biosynthesis protein 7; EC 1.2.1.3 (characterized)
to candidate 3608018 Dshi_1425 aldehyde dehydrogenase (RefSeq)
Query= SwissProt::S0ENH1 (461 letters) >FitnessBrowser__Dino:3608018 Length = 484 Score = 338 bits (868), Expect = 2e-97 Identities = 184/447 (41%), Positives = 273/447 (61%), Gaps = 11/447 (2%) Query: 25 NPLDRSSLWPAPVATGNDVEEAVRSAQEAFPAWSEKTYKQRTELLEKFADLYLVHANEFC 84 NP + AP A+ + VE+A+ +A+ A P W+ + +R + +AD H E Sbjct: 38 NPATDEVVAHAPNASRDQVEQAIAAAKAAQPGWAALSQDERGAYIAAYADALDAHKQELI 97 Query: 85 QLIATECGRTAGN-AAIEVYVAAQWLRYPSKYEIPEEVTEDEKKTSI-VTHEPLGVVAAI 142 L+ TE G+ + A EV A W+R +K + +EV ED + ++ V H PLGVV AI Sbjct: 98 TLLTTEQGKPRHSMATTEVEYAIFWVREVAKRRLEDEVIEDTPEHTVKVAHTPLGVVGAI 157 Query: 143 CPWNFPLMLALGKIAPALATGNCVILKPSPFTPYSSLKLVELAQQVFPPSVLQVLHGHDD 202 PWNFP++L L KIAP L TGN +++KPSP+TP +L+ E+AQQVFP VL V+ G ++ Sbjct: 158 TPWNFPVLLGLWKIAPCLVTGNTMVMKPSPYTPLCTLRFGEIAQQVFPAGVLNVVAGGNE 217 Query: 203 LGPMLVKHPRIQKITFTGSTTTGKQILRDAAETMKRVTLETAGNNASIILPDVNIEAVIP 262 G L +HP I KI+FTGST TG++++ ++ +KR+TLE GN+ +I+LP + + +IP Sbjct: 218 QGAWLTEHPDIAKISFTGSTATGRKVMASSSCNLKRITLELGGNDPAILLPGTDYKPLIP 277 Query: 263 QLAGGLWFNAGQVCIATRRMYIHQDIFDEAVAQLA--EASKDLASGME------PIQNEM 314 L + N+GQ CIA +R+Y+H+ ++D+ + A K + +GM+ PIQN+M Sbjct: 278 TLFDAAYGNSGQWCIAVKRLYVHESLYDDFLRDFVAHAAEKTVGNGMDPNTDLGPIQNKM 337 Query: 315 QLVRLQQALSDANAAGCELLSLGKTEAAEGFFIQPTILKSPPPDADVVQQENFGPIVSCI 374 Q +L+ +D A G + G+ G F+ TI+ +PP D+ VV++E FGPI+ I Sbjct: 338 QYGKLKDLFADVKAQGLSVPLGGEIPDGPGNFVPITIVDNPPKDSRVVREEPFGPILPII 397 Query: 375 KFSSLDEAISLANNSDTGLAASVWSSDVSAARRVAAKLEVGNVYINGPPQPDPYVPFGGH 434 K+S LDE + AN+++ GLAASVW D A VA +LE G V++N +PFGGH Sbjct: 398 KWSDLDEVVRDANDTEFGLAASVWGPDRDTAIGVANRLEAGTVWVNEIHIHGIDIPFGGH 457 Query: 435 KQSGLGVEYGLPGLLSFCQTKSTYLYK 461 KQSG+GVE G GL F TK TY+++ Sbjct: 458 KQSGMGVENGQEGLKEFTNTK-TYMFR 483 Lambda K H 0.316 0.132 0.392 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: 596 Number of extensions: 29 Number of successful extensions: 6 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: 461 Length of database: 484 Length adjustment: 33 Effective length of query: 428 Effective length of database: 451 Effective search space: 193028 Effective search space used: 193028 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: 51 (24.3 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