Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate HSERO_RS05115 HSERO_RS05115 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__HerbieS:HSERO_RS05115 Length = 793 Score = 340 bits (873), Expect = 8e-98 Identities = 192/478 (40%), Positives = 275/478 (57%), Gaps = 16/478 (3%) Query: 16 TYEQPTGLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSW 75 ++E G FI F Q K+ + P++ + + + + + D+D AV+AA AA W Sbjct: 28 SHEASFGHFIAGRFTQPKAD--LDDIDPASGKLLAHLSQGSAADVDAAVQAAQAAL-PGW 84 Query: 76 STSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWT 134 R + LY LA + HA LA +E LDNGK L S+ DV L A +F AGW Sbjct: 85 QALGGHGRARHLYALARTVQRHARLLAVLETLDNGKPLRESRDVDVPLVARHFYHYAGWA 144 Query: 135 DKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAES 194 + + P+GV GQI+PWNFPLLM +WK+ P L G T VLK AE+ Sbjct: 145 QLQESE----------FPDHVPVGVVGQIVPWNFPLLMLAWKIAPALALGNTVVLKPAEN 194 Query: 195 TPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKA 254 T L+AL A L ++AG P GV+N+V+G G T GA + +HP I+K+AFTGST GR I + Sbjct: 195 TSLTALLFAELAQQAGLPAGVLNIVTGDGAT-GAAVVAHPGIQKIAFTGSTEVGRLIREQ 253 Query: 255 AAESNLKKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYD 314 A S K +TLELGGKSP IVF+DAD+ + I+ +V I++N G+VCCAGSR+ VQEGI+D Sbjct: 254 TAGSG-KSLTLELGGKSPFIVFEDADIDAAIEGVVDAIWFNQGQVCCAGSRLLVQEGIHD 312 Query: 315 KIVSEFKNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGN 374 ++ K + LK+G P + + MGA S +QL+++ ++ G +EGA Sbjct: 313 LFIARLKTRMQKLKVGAPLDKCSDMGALISPVQLERVRSLVEQGVREGAQCHQVVLDTPP 372 Query: 375 KGYFIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNL 434 G F PT+ V + +EIFGPV+ F+T +E + LAN+S YGLAA + + + Sbjct: 373 GGCFYPPTLLTGVHPAATVASEEIFGPVLVAMSFRTPDEAVQLANNSRYGLAASIWSETI 432 Query: 435 STAISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVKAVRIG 492 A+ V+ ++ +G +W+N+ N F V FGG +SG GRE G E Y + + + G Sbjct: 433 GLALGVAPQLKAGVVWINSTNQFDAAVGFGGVRESGYGREGGREGCYEYLKPRRQQAG 490 Score = 69.7 bits (169), Expect = 4e-16 Identities = 59/247 (23%), Positives = 107/247 (43%), Gaps = 13/247 (5%) Query: 29 FVQSKSKKTFGTVSPSTE----EEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVRM 84 ++ K + G VS + E + V +DI +AV AA A W+++ P R Sbjct: 521 YIGGKQVRPDGEVSMACHSTQGERLEDVGLGNRKDIRNAVAAAVKA--GGWTSASPHRRA 578 Query: 85 KVLYKLADLIDEHADTLAHIEALDNGKSLMCSKGDVALTAAYFRSCAGWTDKIKGSVIET 144 + LY +A+ + + A A G + ++ +V + + W DK +G+V + Sbjct: 579 QGLYYIAENLSARTEEFARRIASTTGVTADEARAEVDASIKRLFTYGAWADKFEGAVHQP 638 Query: 145 GDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYLAS 204 E IGV G + P PLL + P++ G V+ +E PL A L Sbjct: 639 PMRGVALAMPEAIGVVGVVCPEEKPLLALISLVAPLIAMGNRVVVVPSEQAPLVATDLYQ 698 Query: 205 LIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGS---TATGRHIMKAAAESNLK 261 ++ + P GV+N+V+G ++ H +++ + G +AT + + NLK Sbjct: 699 VLDTSDLPAGVINIVTGKSAELLPVLAEHDEVEALWVRGPAEFSATAERL----STGNLK 754 Query: 262 KVTLELG 268 + ++ G Sbjct: 755 RCFVDHG 761 Lambda K H 0.316 0.133 0.389 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: 899 Number of extensions: 38 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: 495 Length of database: 793 Length adjustment: 38 Effective length of query: 457 Effective length of database: 755 Effective search space: 345035 Effective search space used: 345035 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: 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