Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate GFF501 PGA1_c05130 aldehyde dehydrogenase
Query= uniprot:Q92L07 (510 letters) >FitnessBrowser__Phaeo:GFF501 Length = 476 Score = 227 bits (579), Expect = 6e-64 Identities = 149/435 (34%), Positives = 228/435 (52%), Gaps = 11/435 (2%) Query: 59 IEKADEAFRAWRLVPAPKRGELVRLLGEELRAFKADLGRLVSIEAGKIPSEGLGEVQEMI 118 I A +A W +R +++ +G E+ A KA+LG+L+S E GK EG+GE Sbjct: 45 IAAARDAAPGWASSTPQQRFDVLDAIGTEILARKAELGKLLSREEGKTLPEGIGEAARAG 104 Query: 119 DICDFAVGLSRQLYGLTIATERPGHRMMETWHPLGVVGIISAFNFPVAVWSWNAALALVC 178 I F G + + G + + RPG + T P+GVVG+I+ +NFP+A+ +W A AL Sbjct: 105 QIFKFFAGETLRQAGEILGSVRPGVGVEVTRSPVGVVGLITPWNFPIAIPAWKIAPALAY 164 Query: 179 GDAVVWKPSEKTPLTALACQAILERAIARFGDAPEGLSQVLIGDRA-IGEVLVDHPKVPL 237 GDAVV KP+E TP A A I+ R+ PEG+ ++ G + +G+ LV V Sbjct: 165 GDAVVLKPAELTPGCAHALAEIINRS-----GLPEGVFNIVFGTGSTVGQTLVQSRHVDA 219 Query: 238 VSATGSTRMGREVGPRLAKRFARAILELGGNNAGIVCPSADLDMALRAIAFGAMGTAGQR 297 +S TGS G + + + LE+GG N +V ADL+ A+ A GA + GQR Sbjct: 220 ISFTGSVETGSAIAAACGAQRKKLQLEMGGKNPMVVLDDADLETAVDASLNGAFFSTGQR 279 Query: 298 CTTLRRLFVHESVYDQLVPRLKKAYQSVSVGNPLESAALVGPLVDKAAFDGMQKAIAEAK 357 CT RL V E ++D+ V L + + VGN L+ + +GP+VD+ + + A Sbjct: 280 CTASSRLIVTEGIHDRFVAALGERMTGLRVGNALDDSTQIGPVVDERQLEKDLYYLDVAA 339 Query: 358 NHGGAVTGGERVELGHENGYYVKPALVEMPKQEGPV-LEETFAPILYVMKYSDFDAVLAE 416 + GG V GG+ ++ G+Y+ PALV + + EE F P+ V++ +D+D L Sbjct: 340 SEGGQVLGGQTLQRS-TKGFYLAPALVTETSNDMRINQEEVFGPLASVIRVADYDEALVV 398 Query: 417 HNAVAAGLSSSIFTRDMQESERFLAADGSDCGIANVNIGTSGAEIGGAFGGEKETG-GGR 475 N GLS+ I T ++ + F A ++ G+A VN+ T+G + FGG K + G R Sbjct: 399 ANDTPFGLSAGICTGSLKYATHFKA--HAEAGMAMVNLPTAGVDYHVPFGGTKGSSFGAR 456 Query: 476 ESGSDAWKAYMRRAT 490 E GS A + Y + T Sbjct: 457 EQGSHAKEFYTKVKT 471 Lambda K H 0.317 0.134 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: 576 Number of extensions: 32 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: 510 Length of database: 476 Length adjustment: 34 Effective length of query: 476 Effective length of database: 442 Effective search space: 210392 Effective search space used: 210392 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