Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate WP_011810430.1 VEIS_RS13090 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-16244 (495 letters) >NCBI__GCF_000015565.1:WP_011810430.1 Length = 798 Score = 352 bits (903), Expect = e-101 Identities = 189/461 (40%), Positives = 273/461 (59%), Gaps = 14/461 (3%) Query: 24 FINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQVR 83 FI+ EFV + F +P+TEE + +V DID AV AA A +WS R Sbjct: 37 FIHGEFVAPAQNEYFEVFNPATEERLARVAHGSDADIDQAVAAARQAL-PAWSGLSGHQR 95 Query: 84 MKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGSVI 142 + LY +A + +HA A +E +DNGK++ S+ D+ L +F AGW + Sbjct: 96 ARYLYAIARHLQKHARFFAVLETMDNGKTIRESRDIDIPLVVRHFYHHAGWAQLLDSE-- 153 Query: 143 ETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSALYL 202 + + +GVCGQI+PWNFPLLM +WK+ P L G T VLK AE TPL+AL Sbjct: 154 --------FPAHQAVGVCGQIVPWNFPLLMLAWKVAPALAAGNTVVLKPAEFTPLTALAF 205 Query: 203 ASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNLKK 262 A L E G P GV+N+V+G G T GA + +H + K+AFTGSTA GR I +A A ++ KK Sbjct: 206 AELCVEVGLPAGVLNIVTGDGHT-GASLVNHAGVDKIAFTGSTAVGRLIRRATAGTD-KK 263 Query: 263 VTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEFKN 322 ++LELGGKSP IVFDDAD+ + ++ +V I++N G+VCCAGSRI VQE + + + + Sbjct: 264 LSLELGGKSPFIVFDDADLDAAVEGVVDSIWFNQGQVCCAGSRILVQESVAARFGDKLRA 323 Query: 323 AAESLKIGDPFKEDTFMGAQTSQLQLDKILKYIDIGKKEGATVITGGERFGNKGYFIKPT 382 L+IG+P + +GA ++QL +I + ++ G+ +G + + G+F PT Sbjct: 324 RMRKLRIGNPLDKSNDVGAIVDRVQLQRIRQMVESGRADGLSCWQTALDAPSSGHFFAPT 383 Query: 383 IFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTAISVSN 442 F DV H + ++EIFGPVV F+T++E +ALAN S YGLAA + + N+ ++V+ Sbjct: 384 FFEDVPAAHALAQEEIFGPVVISMGFRTLDEAVALANHSRYGLAASLWSENIDVCLTVAA 443 Query: 443 KINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNY 483 ++ +G +WVN N F FGGY +SG GRE G E + Y Sbjct: 444 QLAAGVVWVNGANMFDAAAGFGGYRESGFGREGGREGMHEY 484 Score = 78.6 bits (192), Expect = 8e-19 Identities = 64/210 (30%), Positives = 94/210 (44%), Gaps = 5/210 (2%) Query: 58 EDIDDAVEAATAAFHSSWSTSDPQVRMKVLYKLADLIDEHADT-LAHIEALDNGKSLMCS 116 +DI +AVE A A +WS + R +VLY A+ + A T +AH++A+D S Sbjct: 560 KDIRNAVETARKA--GNWSQASGHARAQVLYYFAENLGARAQTFIAHLQAIDGISEAAAS 617 Query: 117 KGDVALTAAYFRSCAGWTDKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWK 176 + + A F A DK GSV T H EP GV G P + PLL A Sbjct: 618 QQFEQVLARVFHYAA-MADKHDGSVHSTLTAHVTLAMNEPFGVVGVRSPAHTPLLAALSL 676 Query: 177 LGPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKI 236 P+L TG VL L L ++ + P GV+N+V G ++ H + Sbjct: 677 ALPLLATGNRVVLVPPPDASLMFADLYQVLDTSDMPAGVLNIVWGDSDELAEVLALHDDV 736 Query: 237 KKVAFTGSTATGRHIMKAAAESNLKKVTLE 266 + + G A G ++AA+ NLK ++ Sbjct: 737 DALWYFG-PAAGAARVQAASAGNLKSTWVQ 765 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: 867 Number of extensions: 38 Number of successful extensions: 8 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: 798 Length adjustment: 38 Effective length of query: 457 Effective length of database: 760 Effective search space: 347320 Effective search space used: 347320 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 24 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