Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase
Query= BRENDA::P25553 (479 letters) >FitnessBrowser__Pedo557:CA265_RS14635 Length = 501 Score = 262 bits (670), Expect = 2e-74 Identities = 156/480 (32%), Positives = 259/480 (53%), Gaps = 17/480 (3%) Query: 6 QHPMYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPA 65 Q+ YI G+FV A+ D ++P V ++ ED A+DAA A W + Sbjct: 13 QYDNYIGGKFVAPVKGAYFDNISPIDGKVFTKAAHSTKEDLELAVDAAHEAFKTWSKTSS 72 Query: 66 IERASWLRKISAGIRERASEISALIVEEGGK-IQQLAEVEVAFTADYIDYMAEWARRYEG 124 ER+ L KI+ + + ++A+ + GK +++ ++ D+ Y A R EG Sbjct: 73 TERSIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEG 132 Query: 125 EIIQSDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNN 184 + + D+ ++++ + +GV I+PWNFP + K+APAL GN +V+KP+E TP + Sbjct: 133 SLSELDQNTVSLIVHE-PIGVVAQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAESTPVS 191 Query: 185 AIAFAKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKN 244 + +++ ++ LP GV N+V G G +G+ L NPKV+ + TGS G +M A +N Sbjct: 192 IMVLMELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLVMQYATEN 250 Query: 245 ITKVCLELGGKAPAIVM------DDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIY 298 I V LELGGK+P I DDA L+ AV+ V +N G++C C R+ +Q+ IY Sbjct: 251 IIPVTLELGGKSPNIFFSSVMAEDDAFLDKAVEGAV-MFALNQGEICTCPSRLLIQEDIY 309 Query: 299 DQFVNRLGEAMQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAV 358 ++F+ ++ E +A++ G+P +R + MG + E++ + EEGA V GG+ Sbjct: 310 EKFIAKVIERTKAIKIGSPLDRT-VMMGAQASKIQFEKIAAYIKLGKEEGAEVLTGGEIN 368 Query: 359 E-----GKGYYYPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTS 413 E G GYY PT+ +M I EE FGPVL V F T+E+AI +AND+ YGL + Sbjct: 369 ELPGELGGGYYIKPTIFKG-HNKMRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLYGLGA 427 Query: 414 SIYTQNLNVAMKAIKGLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQ 473 ++T++ + + + ++ G ++N+ + G+++SG+G + K L Y QT+ Sbjct: 428 GVWTRDAHELYQVPRAIQAGRVWVNQYHAYPAGAPFGGYKQSGVGRENHKMMLGHYRQTK 487 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: 534 Number of extensions: 27 Number of successful extensions: 6 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: 501 Length adjustment: 34 Effective length of query: 445 Effective length of database: 467 Effective search space: 207815 Effective search space used: 207815 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: 52 (24.6 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