GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Algiphilus aromaticivorans DG1253

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_043769493.1 U743_RS15500 NAD(P)-dependent alcohol dehydrogenase

Query= BRENDA::W6CX26
         (339 letters)



>NCBI__GCF_000733765.1:WP_043769493.1
          Length = 338

 Score =  373 bits (957), Expect = e-108
 Identities = 182/335 (54%), Positives = 237/335 (70%), Gaps = 2/335 (0%)

Query: 1   MSIIKSYAAKEAGSELELYEYDAGELRPEDVEVQVDYCGICHSDLSMIDNEWGFSQYPLV 60
           M+ I+++AA+ AG  LE ++YDAG L  + VE+ V++CG+CHSDLSM+DNEWG SQYPLV
Sbjct: 1   MTQIRAWAAQTAGGALEEWQYDAGPLADDGVEIAVEHCGLCHSDLSMLDNEWGQSQYPLV 60

Query: 61  AGHEVIGRVAALGSAAQEKGVKVGQRVGVGWTARSCGHCDACISGNQINCLEGAVATILN 120
            GHEV+GRV ALG  A  +G++VGQRVG+GW A SC HC  C  G+   C       I  
Sbjct: 61  PGHEVVGRVRALGRDA--RGLEVGQRVGLGWIAGSCLHCRPCTGGDHHLCPSVEGTIIGR 118

Query: 121 RGGFAEKLRADWQWVIPLPESIDIESAGPLLCGGITVFKPLLMHHITATSRVGVIGIGGL 180
            GGFAE +RA W+WV PLPE++     GPL CGGITVF PL    I  T RVGV+GIGGL
Sbjct: 119 HGGFAEAVRAHWRWVTPLPEALAPAEVGPLFCGGITVFSPLREFGIRPTDRVGVVGIGGL 178

Query: 181 GHIAIKLLHAMGCEVTAFSSNPSKEQEVLAMGADKVVNSRDPDALNALAGQFDLIINTVN 240
           GH+A++   A GCEVTAF+S+P+K +E   MGA +VV+S D  AL A AG+FDLI+ TVN
Sbjct: 179 GHLALQFARAWGCEVTAFTSSPAKAEEARKMGAHEVVDSTDDAALKACAGRFDLILVTVN 238

Query: 241 VDLDWQPYFEALAYGGHFHTVGAVMKPLPVPAFTLIAGDRSISGSATGTPYELRKLMKFA 300
             L W+ Y  ALA  G  H VGAV++P+ V  F L+   RS+S S TG+P  +  ++ FA
Sbjct: 239 ATLPWKRYISALAPRGRLHFVGAVLEPVQVTVFQLLGAQRSVSASPTGSPAAIADMLDFA 298

Query: 301 GRSKVSPTTELFPMSQINEAIQHVRDGKARYRVVL 335
            R  ++PTTE FP++++N+AIQH+RDGKARYRV++
Sbjct: 299 ARHDIAPTTEHFPVARVNDAIQHLRDGKARYRVIV 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: 329
Number of extensions: 13
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: 338
Length adjustment: 28
Effective length of query: 311
Effective length of database: 310
Effective search space:    96410
Effective search space used:    96410
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