GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Phaeobacter inhibens BS107

Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate GFF2678 PGA1_c27200 alcohol dehydrogenase, iron containing

Query= BRENDA::A4IP64
         (395 letters)



>FitnessBrowser__Phaeo:GFF2678
          Length = 381

 Score =  179 bits (454), Expect = 1e-49
 Identities = 121/381 (31%), Positives = 191/381 (50%), Gaps = 13/381 (3%)

Query: 8   FPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTD 67
           +P     G G + +L       G K  L++TD  L  + +       L   G    ++ +
Sbjct: 9   YPTAIKFGAGRIRELAEACATAGMKKPLLVTDKGLADLPVTQSTLDILEAAGLGRAMFCE 68

Query: 68  VVPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTG-- 125
           V P P  +  E  VA  + G  D VI  GGGS LDL K+ A +   +  V D+ ++    
Sbjct: 69  VDPNPNEKNLEAGVAAYKAGDHDGVIAFGGGSGLDLGKMVAFMCGQNRPVWDFEDIGDWW 128

Query: 126 TRTLEKKGLPKILIPTTSGTGSEVTNISVLSLETT--KDVVTHDYLLADVAIVDPQLTVS 183
           TR       P I +PTT+GTGSEV   SV++   T  K ++ H  +L  V I DP+LTV 
Sbjct: 129 TRADADAIAPIIAVPTTAGTGSEVGRASVITDSVTHQKKIIFHPKVLPTVVICDPELTVG 188

Query: 184 VPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARID 243
           +P  +TA TG+DA  H VEA+ S +  P S G+A+  +RL+   L +A A+G+D +AR  
Sbjct: 189 MPKFITAGTGLDAFAHCVEAFSSPHYHPMSQGIALEGMRLVKEYLPRAYADGTDIEARAQ 248

Query: 244 MANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMAD 303
           M + + + G   F  G+  +HA+++P+G  F+  HG +NAV +  V+ +       R   
Sbjct: 249 MMSAAAM-GATAFQKGLGAIHAMSHPIGALFNTHHGTTNAVCMLAVLAFNAPEIADRFKT 307

Query: 304 IFNALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAVQQKR 363
             + LG +  F    E     V+EL      +GIP+ L   G+ E+A+  L K A+    
Sbjct: 308 AADYLGIDGGF----EGVCAYVQELN---DSLGIPRGLSELGVTEAAIPELVKGALIDPS 360

Query: 364 LLARSPLPLLEADIRAIYEAA 384
               +P+ L +A++  +++ A
Sbjct: 361 -CGGNPVVLDQANLTQLFKDA 380


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: 384
Number of extensions: 19
Number of successful extensions: 4
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: 381
Length adjustment: 30
Effective length of query: 365
Effective length of database: 351
Effective search space:   128115
Effective search space used:   128115
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.

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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