GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Sinorhizobium fredii NGR234

Align alcohol dehydrogenase (EC 1.1.1.1); long-chain-alcohol dehydrogenase (EC 1.1.1.192) (characterized)
to candidate WP_015887793.1 NGR_RS08250 iron-containing alcohol dehydrogenase

Query= BRENDA::A4IP64
         (395 letters)



>NCBI__GCF_000018545.1:WP_015887793.1
          Length = 377

 Score =  219 bits (559), Expect = 8e-62
 Identities = 139/386 (36%), Positives = 212/386 (54%), Gaps = 24/386 (6%)

Query: 6   IVFPPLSHVGWGALDQLVPEVKRLGAKHILVITDPMLVK----IGLVDQVTSPLRQEGYS 61
           +V P L   G G  ++L    +  G + +LVI+D         +GL  +VT         
Sbjct: 10  MVRPGLIEFGTGVAERLGTWAESKGFRRVLVISDAFNASRTDVLGLTGEVT--------- 60

Query: 62  VHVYTDVVPEPPLETGEKAVAFARDGKFDLVIGVGGGSALDLAKLAAVLAVHDGSVADYL 121
             VY DV  EP     +  ++ A   + DL++G GGGSA+DLAKL AVL+     +AD +
Sbjct: 61  --VYGDVKAEPDTGDLDCVLSAAEGARADLIVGFGGGSAMDLAKLVAVLSGSSQRLADVV 118

Query: 122 NLTGTRTLEKKGLPKILIPTTSGTGSEVTNISVLSLETTKD--VVTHDYLLADVAIVDPQ 179
                +    + +    +PTTSGTGSE    ++++   TK    V   ++LAD+A++DP 
Sbjct: 119 G--AGKVAGPREIALAQVPTTSGTGSEAGIRALVTDPETKAKLAVESIHMLADIAVIDPA 176

Query: 180 LTVSVPPRVTAATGIDALTHAVEAYVSVNASPTSDGLAVAAIRLISRSLRKAVANGSDKQ 239
           LT +VPP+VTAATG+DA+ H VEA+ +  A P  D  A+  +RL+ R L +AV +G D +
Sbjct: 177 LTFTVPPKVTAATGVDAMAHCVEAFTNRKAHPAVDIYAIEGVRLVGRYLARAVHDGKDAE 236

Query: 240 ARIDMANGSYLAGLAFFNAGVAGVHALAYPLGGQFHIAHGESNAVLLPYVMGYIRQSCTK 299
           AR  ++  S   G        AG HALAYPLG ++H+AHG +NA++ P+V+ +   +  +
Sbjct: 237 ARAGLSLASLYGGYCLGPVNTAGGHALAYPLGTRWHVAHGAANALIFPHVLAFNTPAVPE 296

Query: 300 RMADIFNALGGNSSFLSEVEASYRCVEELERFVADVGIPKTLGGFGIPESALESLTKDAV 359
           + + +  ALG ++S   E+++ +    E   F A +GI   L   G+  + L ++  DA 
Sbjct: 297 KTSAVLEALGLSAS--QEIKSVFDAAHE---FCASLGIEMKLRQLGVLANDLGTMADDAF 351

Query: 360 QQKRLLARSPLPLLEADIRAIYEAAF 385
             +RLL  +P  L  ADI AIYEAAF
Sbjct: 352 AIRRLLDNNPRDLSRADILAIYEAAF 377


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: 369
Number of extensions: 15
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: 377
Length adjustment: 30
Effective length of query: 365
Effective length of database: 347
Effective search space:   126655
Effective search space used:   126655
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 Apr 09 2024. 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