GapMind for catabolism of small carbon sources

 

Aligments for a candidate for etoh-dh-nad in Pedobacter sp. GW460-11-11-14-LB5

Align Choline dehydrogenase; Alcohol dehydrogenase; EC 1.1.1.- (characterized)
to candidate CA265_RS24860 CA265_RS24860 alcohol dehydrogenase

Query= SwissProt::P71017
         (402 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS24860 CA265_RS24860 alcohol
           dehydrogenase
          Length = 382

 Score =  202 bits (513), Expect = 2e-56
 Identities = 119/382 (31%), Positives = 199/382 (52%), Gaps = 10/382 (2%)

Query: 12  KFHTFEIPTVIKHGIGAIKHTGEEVAALGVSKALLVTDPGIYKAGVADPVIESLKEAGIE 71
           K H F  PT I+ G GA+K     ++   +   L+VTDP I +      + E LK  GI 
Sbjct: 5   KIHQFNFPTTIRFGAGAVKELPAYLSEHNLKAPLIVTDPTIAQLPFFKRIAEDLKAKGIA 64

Query: 72  VVLFNKVEPNPPVRLVNEGSELYKKENCNGLVAVGGGSSMDTAKAIGVEATHEGSVLDYE 131
           V +F+ +  NP    V +G+E++   N + ++ +GGG+++D A+AI +   H   +  Y+
Sbjct: 65  VEVFSDIHKNPVKSDVYKGTEVWDATNRDSIIGIGGGAALDVARAIVLRVNHREDLFKYD 124

Query: 132 -AADGKKPLENRIPPLTTIPTTAGTGSEVTQWAVITDEEREFKFNTGGPLIAAHLTIIDP 190
               G   + N +P   TIPTT+GTGSEV + A+I D+E   K     P + A +   DP
Sbjct: 125 DLIGGDIYVTNDVPHFITIPTTSGTGSEVGRSAIIADDETHQKKILFSPKLMAQIVFADP 184

Query: 191 ELHVSMPPHVTAMTGIDALAHAIECYTMKFAQPITDAVALMAIEYAAHYIKRAFADGEDL 250
           EL + +PP +TA TG+DAL H +E Y  K   P+ D +AL  I      ++RA  +  DL
Sbjct: 185 ELTMDLPPFITAATGMDALTHNMEAYLAKNFHPMCDGIALEGISLIKDALERA-TNNPDL 243

Query: 251 EARYGMAQAAMLAGLSYGSESAGAAHAMSQTLGGIIPVAHGQCVAAMMGPVMEYNWKGYP 310
           E+R  M  A+M+  +++  +  G  H+++  L  ++   HG   A  +   M++N  G+ 
Sbjct: 244 ESRSKMLMASMMGAIAF-QKGLGVVHSLAHPLSSLLDTHHGLANAVNIPYGMQFNIAGFE 302

Query: 311 EKFARIAKAFGIDTSKMTTEEAAKASVNWMYDLVEDLEVP-TLEEQGVSPDMIERLSKEA 369
           ++F +IA+   +       +E  +A V +++DL   + +P  L + GV  + IE L+  A
Sbjct: 303 DRFKKIARTLDL------KDENGEAVVKYLFDLNTKVNIPHKLSDIGVKNEHIETLADLA 356

Query: 370 MKDPQTFGNPRDLNEKAYNWIY 391
             D     NP+ ++   +  +Y
Sbjct: 357 FADFAHPNNPKPVSRADFKQLY 378


Lambda     K      H
   0.315    0.132    0.384 

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: 379
Number of extensions: 13
Number of successful extensions: 3
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: 402
Length of database: 382
Length adjustment: 31
Effective length of query: 371
Effective length of database: 351
Effective search space:   130221
Effective search space used:   130221
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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