Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate WP_013459096.1 SULKU_RS01190 aldehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >NCBI__GCF_000183725.1:WP_013459096.1 Length = 471 Score = 231 bits (589), Expect = 4e-65 Identities = 153/459 (33%), Positives = 238/459 (51%), Gaps = 17/459 (3%) Query: 27 VNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERASEI 86 ++P V+SR + A+DAR+A+ A+ A + + +R +WL +++ ++E+ E Sbjct: 21 LSPYDGRVVSRAAECSADDARQALIIAQNASKIAKKVALHQRCAWLLDVASKLKEQREEF 80 Query: 87 SALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQSDRP----GENILLFKRA 142 + ++ +E GK A +EV + I AE R GE I +D + + A Sbjct: 81 ARVLCDEVGKPITYARIEVDRCIETITLSAETMRTMHGESINTDAMPSGRAAHAYWRREA 140 Query: 143 LGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKI-VDEIGLPRGV 201 GV I P+NFP L+A K+APAL+ GN +V+KP+ P A A++ ++ Sbjct: 141 AGVVVAITPFNFPLNLVAHKLAPALVAGNAVVLKPTPEAPLCAYKLAQLFIESPYATPDA 200 Query: 202 FNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIVM 261 ++V G E VG L G+ ++S TGSV G I T + I K+ LELGG A + Sbjct: 201 LSVVYGDAE-VGSALVGSDIPRVISFTGSVGVGNII--TRSAGIKKISLELGGNAATYID 257 Query: 262 DDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAERN 321 ADLE A +NSGQVC +R+YV +YD+F ++ EA + G+P + Sbjct: 258 TSADLEYAAARCAIGAFVNSGQVCISLQRIYVDSSVYDEFALKMAEATSKLVVGSP-YND 316 Query: 322 DIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTLLLDVRQEMSIMH 381 D +GPLIN A R V A+EEGAR A EG+ +Y P ++ DV + M I+ Sbjct: 317 DTFLGPLINDEAASRAMSWVESAIEEGAR-ALTPPRCEGRIFY--PCVMADVTESMKIVC 373 Query: 382 EETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGETYIN--- 438 EE F P++ +V D ++DAI+ N+S YGL S++T NL+ A KAI L G IN Sbjct: 374 EEVFAPIVSLVRVDGIDDAITRMNNSPYGLQFSVFTNNLSHATKAIDELDAGGVVINDMP 433 Query: 439 RENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYL 477 F+ + G + SG+G + + E+ + + + + Sbjct: 434 TLRFDIQP--YGGVKLSGVGREGPRFAIEEFTEIKSIVI 470 Lambda K H 0.318 0.135 0.392 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: 448 Number of extensions: 21 Number of successful extensions: 5 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: 479 Length of database: 471 Length adjustment: 33 Effective length of query: 446 Effective length of database: 438 Effective search space: 195348 Effective search space used: 195348 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 (21.7 bits) S2: 51 (24.3 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