GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Pseudovibrio axinellae Ad2

Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate WP_068009207.1 PsAD2_RS18125 iron-containing alcohol dehydrogenase

Query= BRENDA::A4IP64
         (395 letters)



>NCBI__GCF_001623255.1:WP_068009207.1
          Length = 387

 Score =  188 bits (478), Expect = 2e-52
 Identities = 123/382 (32%), Positives = 195/382 (51%), Gaps = 13/382 (3%)

Query: 3   VARIVFPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVKIGLVDQVTSPLRQEGYSV 62
           +A   +P     G G + +L       G K  L++TD  L  + +       +   G   
Sbjct: 4   IANWSYPTAIRFGAGRIKELAEACTAAGMKKPLLVTDKGLANLPITSSTLDIMEAAGLGR 63

Query: 63  HVYTDVVPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYLN 122
            +++DV P P     E  VA  + G  D VI  GGGS LDL KL A  A    SV D+ +
Sbjct: 64  GLFSDVDPNPSEINLEAGVAAFKAGDHDGVIAFGGGSGLDLGKLIAFQAGQTRSVWDFED 123

Query: 123 LTG--TRTLEKKGLPKILIPTTSGTGSEVTNISVLSLETT--KDVVTHDYLLADVAIVDP 178
           +    TR       P I IPTT+GTGSEV   SVL+   T  K ++ H  +L  V I DP
Sbjct: 124 IGDWWTRADADAIYPNIAIPTTAGTGSEVGRASVLTNSQTHVKKIIFHPKILPSVVICDP 183

Query: 179 QLTVSVPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDK 238
           +LTV +P  +T  TGIDA  H++EA+ S +  P S G+A+  +RL+  +L +  A+ +D 
Sbjct: 184 ELTVGMPQMITVGTGIDAFVHSLEAFCSPHYHPMSQGIALEGMRLVKDNLPRVFADPNDI 243

Query: 239 QARIDMANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCT 298
           +AR  M + + +  +A F  G+ G+HALA+P+G  ++  HG +NAV++P V+ + R +  
Sbjct: 244 EARGHMMSAAAMGAVA-FQKGLGGIHALAHPVGAVYNTHHGMTNAVIMPAVLKFNRSAVE 302

Query: 299 KRMADIFNALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDA 358
           +R+  +   LG +  F    +  Y  V ++     D+G+P+ L   G+    ++ L  +A
Sbjct: 303 ERIEMLAAYLGISGGF----DGFYEFVMKMRE---DMGVPQNLSALGVGTDKVDVLAAEA 355

Query: 359 VQQKRLLARSPLPLLEADIRAI 380
           ++       +P+ L     RA+
Sbjct: 356 IKDPS-AGGNPIALTHEAARAL 376


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: 372
Number of extensions: 27
Number of successful extensions: 5
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: 387
Length adjustment: 31
Effective length of query: 364
Effective length of database: 356
Effective search space:   129584
Effective search space used:   129584
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 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