GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Pseudomonas fluorescens FW300-N2E3

Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate AO353_24900 AO353_24900 alcohol dehydrogenase

Query= BRENDA::A4IP64
         (395 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_24900
          Length = 386

 Score =  191 bits (484), Expect = 4e-53
 Identities = 125/390 (32%), Positives = 197/390 (50%), Gaps = 20/390 (5%)

Query: 8   FPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSVHVYTD 67
           +P   H G G + +L    +  G +  L++TD  L +  +       LR  G  V ++ D
Sbjct: 9   YPTSIHFGVGRIAELADTCRSQGIQRPLLVTDSGLARAPITTAALESLRAAGLGVELFCD 68

Query: 68  VVPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLNLTG-- 125
           + P P        +   R GK D V+  GGGS LD+ KL A ++     V D+ ++    
Sbjct: 69  LKPNPVEANLAGGLDAWRAGKHDGVVAFGGGSGLDMGKLIAFMSGQTRPVWDFEDIGDYW 128

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

Query: 184 VPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQARID 243
           +P +VTA TG+DA  H +E+Y +    P ++G+AV  +RL++ +L +AV   SD +AR +
Sbjct: 189 MPAKVTAGTGMDAFAHCLESYCAPGFHPMAEGIAVEGMRLVANALVRAVRTPSDLEARAE 248

Query: 244 MANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTKRMAD 303
           M   + + G   F  G+ G+HALA+P+G  +   HG +NA  +PYV+ + R +  +R+  
Sbjct: 249 MLAAAAM-GATAFQKGLGGMHALAHPVGALYDTHHGMTNATFMPYVLKFNRPAIEERITR 307

Query: 304 IFNAL----GGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAV 359
           +   L     G  SFL+ V           +   D+G+P TL   G+ +   + +   A+
Sbjct: 308 LAAYLRLPTPGFDSFLAFV----------LKLRKDIGVPHTLFELGVDDRQADLIADMAI 357

Query: 360 QQKRLLARSPLPLLEADIRAIYEAAFAGTI 389
                   +PLPL       I+EAA+ G +
Sbjct: 358 VDP-CAGGNPLPLTRNGAMEIFEAAYHGRL 386


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: 379
Number of extensions: 25
Number of successful extensions: 6
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: 386
Length adjustment: 31
Effective length of query: 364
Effective length of database: 355
Effective search space:   129220
Effective search space used:   129220
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