Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate HSERO_RS19755 HSERO_RS19755 betaine-aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__HerbieS:HSERO_RS19755 Length = 484 Score = 390 bits (1003), Expect = e-113 Identities = 213/477 (44%), Positives = 286/477 (59%), Gaps = 6/477 (1%) Query: 38 QIFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMD 97 Q FI E +A + VNP E+ A+G DV +AV AA+A + G W ++ Sbjct: 6 QHFIAGEATEASDGQRMNLVNPINEEIYASAAQGTAADVARAVAAAKAQLE-GGAWSKLS 64 Query: 98 ASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYH 157 RG+LL++LA L+ERD LA ++ G+ + ++D+ + LR AGWA++ Sbjct: 65 GLQRGQLLHKLAALVERDTDLLADMDARAIGRSPMEPRMMDVPNAISHLRAAAGWANQME 124 Query: 158 GKTIPIDGDF----FSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQ 213 G+TIP G SYT EP+GV G I+PWN PL++ +WK+ LA G VV+K AE+ Sbjct: 125 GRTIPTAGYMGKPTLSYTVREPIGVVGAILPWNAPLMITSWKVAALLAAGCTVVIKPAEE 184 Query: 214 TPLTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVA 273 TP +AL++A L +EAGFP GV+N+V G+G + G A+ H DV K++FTGS E GR IQ Sbjct: 185 TPQSALHLARLAQEAGFPDGVINVVTGYGNSVGRALCEHPDVAKISFTGSPEAGRAIQRI 244 Query: 274 AGSSNLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYD 333 AG KRVTLELGGKSP I+ DA + A+ LF NQGQ C AGSR VQ + Sbjct: 245 AGEQ-FKRVTLELGGKSPQIVFDDAPFEDALFGCTLGLFVNQGQVCAAGSRILVQRSLAQ 303 Query: 334 EFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAAD 393 F + A VG+P GP + QF+++ YI G EGA LL GG D Sbjct: 304 RFAKALAEAAAGITVGDPSQPGVRMGPVAKKAQFERVNRYIQQGLDEGATLLAGGVSRPD 363 Query: 394 RGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDL 453 +G+F+QPT+F D +GM+IA+EEIFGPV I+ F T EE + AN+S YGLAA V+T +L Sbjct: 364 KGWFVQPTIFADANNGMSIAREEIFGPVGTIISFDTEEEAIALANDSKYGLAATVWTTNL 423 Query: 454 DKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTV 510 +A+ ++ ++ G V VNC+ A P+GG K SG GRE G G AYTE KTVTV Sbjct: 424 ARAHRVAAGVKVGAVGVNCWSPLDANLPWGGIKDSGMGREGGLAGALAYTEEKTVTV 480 Lambda K H 0.319 0.136 0.409 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: 609 Number of extensions: 20 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: 517 Length of database: 484 Length adjustment: 34 Effective length of query: 483 Effective length of database: 450 Effective search space: 217350 Effective search space used: 217350 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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