Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate PP_2049 PP_2049 Alcohol dehydrogenase, iron-containing
Query= BRENDA::A4IP64 (395 letters) >FitnessBrowser__Putida:PP_2049 Length = 387 Score = 242 bits (617), Expect = 2e-68 Identities = 149/372 (40%), Positives = 219/372 (58%), Gaps = 4/372 (1%) Query: 17 GALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTDVVPEPPLET 76 GA+ +L + GAK +L+I+DP + ++G++D + V ++++V +P Sbjct: 17 GAVQRLAGLCRERGAKRVLIISDPGIARLGMLDDLLPGFTAAKVGVAIFSEVTADPSEAC 76 Query: 77 GEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTGTRTLEKKGLPK 136 A AR DLV+G GGGS++D+AKL A+LA D S L G + + LP Sbjct: 77 VLAAAQRARHIGADLVVGFGGGSSMDVAKLVALLAHRDCS-QPIAELYGIDRAKGRRLPL 135 Query: 137 ILIPTTSGTGSEVTNISVLSL-ETTKDVVTHDYLLADVAIVDPQLTVSVPPRVTAATGID 195 I +PTT+GTGSEVT I++++ TTK + LL D+A++D T+ +P VTAATGID Sbjct: 136 IQVPTTAGTGSEVTPIAIVTTGATTKMGIVSPLLLPDLAVLDAVCTLGLPSAVTAATGID 195 Query: 196 ALTHAVEAYVS-VNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARIDMANGSYLAGLA 254 A+ HA+EAY S + +P S LA A+RL++ +L +AV NG + QAR M G+ LAG A Sbjct: 196 AMVHAIEAYTSRLKRNPLSSLLAREALRLLADNLDQAVHNGGNLQARQAMLLGACLAGQA 255 Query: 255 FFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMADI-FNALGGNSS 313 F NA VA VHALAYPLGG FH+ HG +NA++LP+V+ + A++ LG Sbjct: 256 FANAPVAAVHALAYPLGGHFHVPHGLANALVLPHVLRFNLPVAAVDYAELAVPLLGARLQ 315 Query: 314 FLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKRLLARSPLPLL 373 + + + + V EL + G+P L +P L L +DA+QQ+RLL +P + Sbjct: 316 PGDQRQQAEQFVAELAALSSRCGLPDRLRDADVPRHRLGQLAEDAMQQQRLLVNNPREVT 375 Query: 374 EADIRAIYEAAF 385 +AD AIYEAA+ Sbjct: 376 QADALAIYEAAY 387 Lambda K H 0.318 0.135 0.381 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: 381 Number of extensions: 19 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: 395 Length of database: 387 Length adjustment: 31 Effective length of query: 364 Effective length of database: 356 Effective search space: 129584 Effective search space used: 129584 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: 50 (23.9 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