GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-c in Herbaspirillum seropedicae SmR1

Align alcohol dehydrogenase (cytochrome c) (EC 1.1.2.8) (characterized)
to candidate HSERO_RS06965 HSERO_RS06965 alcohol dehydrogenase

Query= BRENDA::C7G3B8
         (472 letters)



>FitnessBrowser__HerbieS:HSERO_RS06965
          Length = 422

 Score =  272 bits (696), Expect = 1e-77
 Identities = 150/393 (38%), Positives = 222/393 (56%), Gaps = 15/393 (3%)

Query: 34  IKKGEYVARLGDCVACHTSLNGQKYAGGLSIKTPIGTIYSTNITPDPTYGIGTYTFKEFD 93
           + +G+Y+AR G+C+ACHT+  G  YAGG +I +P GT+Y++NITPD T GIG ++  +F 
Sbjct: 39  LAQGQYLARAGNCMACHTARGGAPYAGGRAIASPFGTLYTSNITPDKTTGIGQWSADDFW 98

Query: 94  EAVRHGVRKDGATLYPAMPYPSFARMTQDDMKALYAYFMHGAQPIAQKNHPTDISWPMSM 153
            A+ HG  K+G  LYPA PY S+ R+++ D  AL+AY +    P+A+ N    + +P   
Sbjct: 99  RALHHGRGKEGQFLYPAFPYTSYTRLSRADSDALFAY-LQSLPPVARANQAHTLRFPYDQ 157

Query: 154 RWPLSIWRSVFAPAPKDFTPAPGTDAEIARGEYLVTGPGHCGACHTPRGFGMQEKALDAS 213
           R  L +WR+++   P+ + P P  DA+  RG YLV G GHC ACH+ R        L AS
Sbjct: 158 RMLLGLWRALYF-TPQSYQPDPRQDAQWNRGAYLVQGAGHCSACHSAR------NRLGAS 210

Query: 214 GGPDFLGGGGV-IDNWIAPSLRNDPVLGLGRWSDEDLFLFLKSGRTDHSAAFGGMADVVG 272
             P  L GG +    W AP L      GL  WS  D+   LK+G + H+   G M+++VG
Sbjct: 211 IEPLALAGGVIPALQWYAPPLHGG-ADGLQDWSTADIAALLKTGVSPHAVTLGPMSEIVG 269

Query: 273 WSTQYFTDADLHAMVKYIKSLPPVPPARGDYSYDASTAQMLDSNNISGNAGAKTYVDQCA 332
            S QY  DAD+ AM  Y+KSL   P +  D +   ++ +  ++  I    G + Y   C 
Sbjct: 270 RSLQYLNDADVSAMAVYLKSL---PASAADDAARPASVEPAEAERIM-KQGKQLYGTLCV 325

Query: 333 ICHRNDGGGVARMFPPLAGNPVVVSDNPTSVAHIVVDGGVLPPTNWAPSAVAMPDYKNIL 392
            CH   G G A  +PPLAGN  +   +P +    V++GG  P T   P    MP +   L
Sbjct: 326 DCHGGKGQGSAPDYPPLAGNRAIAGPHPANAVRAVLNGGFPPSTAGNPYPFGMPPFGPQL 385

Query: 393 SDQQIADVVNFIRSAWGNRAPANTTAADIQKLR 425
           SDQ++A VV+++R++WGN+     +AA++ + R
Sbjct: 386 SDQEVAAVVSYVRNSWGNQG-GLVSAAEVNRYR 417



 Score = 55.1 bits (131), Expect = 5e-12
 Identities = 38/131 (29%), Positives = 58/131 (44%), Gaps = 18/131 (13%)

Query: 172 TPAPGTDAEIARGEYLVTGPGHCGACHTPRGFGMQEKALDASGGPDFLGGGGVIDNW--- 228
           TPAP    ++A+G+YL    G+C ACHT R            GG  + GG  +   +   
Sbjct: 30  TPAPDPTRQLAQGQYLARA-GNCMACHTAR------------GGAPYAGGRAIASPFGTL 76

Query: 229 IAPSLRNDPVLGLGRWSDEDLFLFLKSGRTDHSAAFGGMADVVGWSTQYFTDADLHAMVK 288
              ++  D   G+G+WS +D +  L  GR               ++    + AD  A+  
Sbjct: 77  YTSNITPDKTTGIGQWSADDFWRALHHGRGKEGQFLYPAFPYTSYTR--LSRADSDALFA 134

Query: 289 YIKSLPPVPPA 299
           Y++SLPPV  A
Sbjct: 135 YLQSLPPVARA 145


Lambda     K      H
   0.318    0.135    0.430 

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: 759
Number of extensions: 59
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 472
Length of database: 422
Length adjustment: 33
Effective length of query: 439
Effective length of database: 389
Effective search space:   170771
Effective search space used:   170771
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: 51 (24.3 bits)

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

Links

Downloads

Related tools

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