GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Arenitalea lutea P7-3-5

Align alcohol dehydrogenase (EC 1.1.1.1); aryl-alcohol dehydrogenase (EC 1.1.1.90); aryl-alcohol dehydrogenase (NADP+) (EC 1.1.1.91) (characterized)
to candidate WP_019388773.1 P735_RS0114520 NAD(P)-dependent alcohol dehydrogenase

Query= BRENDA::W6CX26
         (339 letters)



>NCBI__GCF_000283015.1:WP_019388773.1
          Length = 334

 Score =  366 bits (940), Expect = e-106
 Identities = 164/333 (49%), Positives = 233/333 (69%), Gaps = 2/333 (0%)

Query: 4   IKSYAAKEAGSELELYEYDAGELRPEDVEVQVDYCGICHSDLSMIDNEWGFSQYPLVAGH 63
           +  YAA E  ++L  + Y+ GE+  E+V+++V YCGICHSDLSMI+N+WG +QYP+V GH
Sbjct: 3   VNGYAALEQKAKLVPFSYELGEIGSEEVDIKVSYCGICHSDLSMINNDWGMTQYPMVPGH 62

Query: 64  EVIGRVAALGSAAQEKGVKVGQRVGVGWTARSCGHCDACISGNQINCLEGAVATILNRGG 123
           E+IG V A G+A   K + VG +VG+GW + SC  CD C+ G    C +     +   GG
Sbjct: 63  EIIGEVIAKGNAV--KNISVGDKVGLGWMSASCMSCDQCMDGEHHLCAKSEATIVGRNGG 120

Query: 124 FAEKLRADWQWVIPLPESIDIESAGPLLCGGITVFKPLLMHHITATSRVGVIGIGGLGHI 183
           FA+K+R  W W IPLP+ ID+  AGPLLCGGITVF P+++  +  T RVGVIGIGGLGH+
Sbjct: 121 FADKVRGHWSWAIPLPKGIDMSKAGPLLCGGITVFNPIILAGVKPTDRVGVIGIGGLGHM 180

Query: 184 AIKLLHAMGCEVTAFSSNPSKEQEVLAMGADKVVNSRDPDALNALAGQFDLIINTVNVDL 243
           A+K L   GCEV AFSSNP+K++ +L MGA +V++S  P+ L +++G+ + I+NT NV L
Sbjct: 181 AVKFLKHWGCEVIAFSSNPAKKKSILKMGASQVIDSTSPEELESISGKLNFILNTTNVSL 240

Query: 244 DWQPYFEALAYGGHFHTVGAVMKPLPVPAFTLIAGDRSISGSATGTPYELRKLMKFAGRS 303
           DW  Y   LA  G FHTVGAV++P+ + AF+LI G++S+ GS  G+P   + ++ F  R 
Sbjct: 241 DWNSYLATLAPKGKFHTVGAVLEPMEISAFSLIMGEKSVGGSPIGSPALTKTMLDFCVRH 300

Query: 304 KVSPTTELFPMSQINEAIQHVRDGKARYRVVLQ 336
            + P  E FPM+++NEA++H+  GKAR+R+VL+
Sbjct: 301 NIYPDVEEFPMAKVNEALEHLEKGKARFRIVLK 333


Lambda     K      H
   0.320    0.137    0.415 

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: 312
Number of extensions: 12
Number of successful extensions: 2
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: 339
Length of database: 334
Length adjustment: 28
Effective length of query: 311
Effective length of database: 306
Effective search space:    95166
Effective search space used:    95166
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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:

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