Align NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate GFF3227 PGA1_c32800 aldehyde dehydrogenase
Query= metacyc::MONOMER-16244 (495 letters) >FitnessBrowser__Phaeo:GFF3227 Length = 802 Score = 327 bits (838), Expect = 1e-93 Identities = 191/470 (40%), Positives = 272/470 (57%), Gaps = 25/470 (5%) Query: 22 GLFINNEFVQSKSKKTFGTVSPSTEEEITQVYEAFSEDIDDAVEAATAAFHSSWSTSDPQ 81 G FIN EF F + +P+T E + + +A D+D AV+AA A + WS + Sbjct: 58 GHFINGEFTAPGDG--FDSKNPATGEVLATLSQATQSDVDSAVDAARKA-QTKWSAAGGA 114 Query: 82 VRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSKG-DVALTAAYFRSCAGWTDKIKGS 140 R + LY +A L+ +HA A +E LDNGK + S+ DV L +F AG ++ Sbjct: 115 ARARYLYAIARLMQKHARLFAVLETLDNGKPIRESRDIDVPLAQRHFYYHAGMAQLMESE 174 Query: 141 VIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKLGPVLCTGCTTVLKTAESTPLSAL 200 + + RE +GVCGQIIPWNFPLLM +WK+ P + G T VLK AE T L+AL Sbjct: 175 LPD----------REALGVCGQIIPWNFPLLMLAWKVAPAIAMGNTVVLKPAEYTSLTAL 224 Query: 201 YLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIKKVAFTGSTATGRHIMKAAAESNL 260 A + ++AG P GVVN+V+G G + + + K+AFTGSTA GR I +A A S Sbjct: 225 LFADICRQAGLPKGVVNIVTGDGAVGEMIVGAD--VDKIAFTGSTAVGRRIREATAGSG- 281 Query: 261 KKVTLELGGKSPNIVFDDADVKSTIQHLVTGIFYNTGEVCCAGSRIYVQEGIYDKIVSEF 320 K +TLELGGKSP IVFDDAD+ S I+ LV I++N G+VCCAGSR+ VQEGI ++ ++ Sbjct: 282 KALTLELGGKSPYIVFDDADIDSAIEGLVDAIWFNQGQVCCAGSRLLVQEGIAERFHTKL 341 Query: 321 KNAAESLKIGDPFKEDTFMGAQTSQLQLDKILKYI---DIGKKEGATVITGGERFGNKGY 377 + + L+IG+P + +GA +QL I + + G+ A V +G Sbjct: 342 RVRMDKLRIGNPLDKSIDVGAIVDPVQLTTISEMVAANTAGRMHQAQVAVP-----ERGC 396 Query: 378 FIKPTIFGDVKEDHQIVRDEIFGPVVTITKFKTVEEVIALANDSEYGLAAGVHTTNLSTA 437 F PT+ + ++++EIFGPV+ T F+T E + LAN++ YGLAA + T N++ A Sbjct: 397 FYPPTLIEGLAPSDALMQEEIFGPVLVSTTFRTPSEAVELANNTRYGLAATLWTENVNLA 456 Query: 438 ISVSNKINSGTIWVNTYNDFHPMVPFGGYSQSGIGREMGEEALDNYTQVK 487 + ++ K+ +G +WVN N F FGG +SG GRE G E L YT+ K Sbjct: 457 LDIAPKLVAGVVWVNATNLFDAAAGFGGTRESGFGREGGWEGLSAYTKPK 506 Score = 77.0 bits (188), Expect = 2e-18 Identities = 55/212 (25%), Positives = 100/212 (47%), Gaps = 7/212 (3%) Query: 58 EDIDDAVEAATAAFHSSWSTSDPQVRMKVLYKLADLIDEHADTLAHIEALDNGKSLMCSK 117 +D+ +AVEAA A ++WS + +R ++LY + + + A GKS + Sbjct: 568 KDVRNAVEAAAGA--NAWSKTTGHLRAQILYYIGENLSARVGEFADRIDRMTGKSQGAQE 625 Query: 118 GDVALTAAYFRSCAGWTDKIKGSVIETGDTHFNYTRREPIGVCGQIIPWNFPLLMASWKL 177 + ++ + + A W DK G +EP+GV G + PLL + Sbjct: 626 VEASIQRLF--TAAAWADKYDGQAHGVPIRGVALAMKEPVGVIGALCADEAPLLGLVSVM 683 Query: 178 GPVLCTGCTTVLKTAESTPLSALYLASLIKEAGAPPGVVNVVSGFGPTAGAPISSHPKIK 237 P + G VL +E+ PLSA +++ + P GVVN+++G +P++SH + Sbjct: 684 APAIAMGNRVVLAASEAYPLSATDFYQVLETSDLPGGVVNILTGRHAEMASPLASHLNVD 743 Query: 238 KV-AFTGSTATGRHIMKAAAESNLKKVTLELG 268 V +F+ S + +++ A+ NLK+ + G Sbjct: 744 AVWSFSSSDLSA--MIEEASAGNLKRTWVNNG 773 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: 891 Number of extensions: 43 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: 802 Length adjustment: 38 Effective length of query: 457 Effective length of database: 764 Effective search space: 349148 Effective search space used: 349148 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