Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate HSERO_RS05115 HSERO_RS05115 aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__HerbieS:HSERO_RS05115 Length = 793 Score = 353 bits (906), Expect = e-101 Identities = 197/446 (44%), Positives = 268/446 (60%), Gaps = 15/446 (3%) Query: 57 VNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLADLIERDR 116 ++P++G+++ +++G DVD AV+AA+AA W+ + R R L LA ++R Sbjct: 51 IDPASGKLLAHLSQGSAADVDAAVQAAQAALP---GWQALGGHGRARHLYALARTVQRHA 107 Query: 117 TYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKTIPIDGDFFSYTRHEPV 176 LA LETLDNGKP S VD+ +V + +YAGWA + + H PV Sbjct: 108 RLLAVLETLDNGKPLRESRDVDVPLVARHFYHYAGWAQLQESE----------FPDHVPV 157 Query: 177 GVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAGFPPGVVN 236 GV GQI+PWNFPLLM AWK+ PALA GN VV+K AE T LTAL A L ++AG P GV+N Sbjct: 158 GVVGQIVPWNFPLLMLAWKIAPALALGNTVVLKPAENTSLTALLFAELAQQAGLPAGVLN 217 Query: 237 IVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNLKRVTLELGGKSPNIIMS 296 IV G G T GAA+ +H + K+AFTGSTE+GR+I+ S K +TLELGGKSP I+ Sbjct: 218 IVTGDGAT-GAAVVAHPGIQKIAFTGSTEVGRLIREQTAGSG-KSLTLELGGKSPFIVFE 275 Query: 297 DADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARAKSRVVGNPFDSKT 356 DAD+D A+E A++FNQGQ CCAGSR VQE I+D F+ R R + VG P D + Sbjct: 276 DADIDAAIEGVVDAIWFNQGQVCCAGSRLLVQEGIHDLFIARLKTRMQKLKVGAPLDKCS 335 Query: 357 EQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADRGYFIQPTVFGDVQDGMTIAKEE 416 + G + Q +++ + G +EGA+ G F PT+ V T+A EE Sbjct: 336 DMGALISPVQLERVRSLVEQGVREGAQCHQVVLDTPPGGCFYPPTLLTGVHPAATVASEE 395 Query: 417 IFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQALQAGTVWVNCYDVF 476 IFGPV+ + F+T +E V ANNS YGLAA+++++ + A ++ L+AG VW+N + F Sbjct: 396 IFGPVLVAMSFRTPDEAVQLANNSRYGLAASIWSETIGLALGVAPQLKAGVVWINSTNQF 455 Query: 477 GAQSPFGGYKMSGSGRELGEYGLQAY 502 A FGG + SG GRE G G Y Sbjct: 456 DAAVGFGGVRESGYGREGGREGCYEY 481 Score = 75.9 bits (185), Expect = 5e-18 Identities = 62/226 (27%), Positives = 96/226 (42%), Gaps = 6/226 (2%) Query: 62 GEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLADLIERDRTYLAA 121 GE + V G+++D+ AV AA A W R + L +A+ + RT A Sbjct: 542 GERLEDVGLGNRKDIRNAVAAAVKA----GGWTSASPHRRAQGLYYIAENLSA-RTEEFA 596 Query: 122 LETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKTIPIDGDFFSYTRHEPVGVCGQ 181 ++D +K L Y WADK+ G + E +GV G Sbjct: 597 RRIASTTGVTADEARAEVDASIKRLFTYGAWADKFEGAVHQPPMRGVALAMPEAIGVVGV 656 Query: 182 IIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAGFPPGVVNIVPGF 241 + P PLL + P +A GN VV+ +EQ PL A + ++ + P GV+NIV G Sbjct: 657 VCPEEKPLLALISLVAPLIAMGNRVVVVPSEQAPLVATDLYQVLDTSDLPAGVINIVTGK 716 Query: 242 GPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNLKRVTLELG 287 +A H++V+ + G E + + NLKR ++ G Sbjct: 717 SAELLPVLAEHDEVEALWVRGPAEFSATAE-RLSTGNLKRCFVDHG 761 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: 952 Number of extensions: 51 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 517 Length of database: 793 Length adjustment: 38 Effective length of query: 479 Effective length of database: 755 Effective search space: 361645 Effective search space used: 361645 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: 54 (25.4 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