GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxaB in Amantichitinum ursilacus IGB-41

Align tagaturonate reductase (EC 1.1.1.58) (characterized)
to candidate WP_053935922.1 WG78_RS01025 tagaturonate reductase

Query= ecocyc::ALTRO-OXIDOREDUCT-MONOMER
         (483 letters)



>NCBI__GCF_001294205.1:WP_053935922.1
          Length = 477

 Score =  488 bits (1255), Expect = e-142
 Identities = 255/468 (54%), Positives = 320/468 (68%), Gaps = 4/468 (0%)

Query: 15  PERIIQFGEGNFLRAFVDWQIDLLNEHTDLNSGVVVVRPIETSFPPSLSTQDGLYTTIIR 74
           P R +QFGEGNFLRAF+DWQIDLLNE   L++ VV+VRPI     P L+TQ G+YTT+IR
Sbjct: 13  PIRFVQFGEGNFLRAFIDWQIDLLNERVGLDASVVIVRPIARPDMPLLNTQGGVYTTLIR 72

Query: 75  GLNEKGEAVSDARLIRSVNREISVYSEYDEFLKLAHNPEMRFVFSNTTEAGISYHAGDKF 134
           GLNE G  V + R I+ V  E+   + +++ L LAH P +RFV SNTTEAGI  +  D F
Sbjct: 73  GLNEDGVPVKEYRQIQCVKGEVDATARWNDVLALAHVPSLRFVVSNTTEAGICINNTDGF 132

Query: 135 DDAPAVSYPAKLTRLLFERFSHFNGALDKGWIIIPCELIDYNGDALRELVLRYAQEWALP 194
           +D P  S+PAKLTR LFER+ HF GA DKG +++PCELID+NGDAL++ V+ +A  W L 
Sbjct: 133 EDFPPSSFPAKLTRFLFERYRHFEGATDKGVVLLPCELIDHNGDALKQAVIHFAALWKLG 192

Query: 195 EAFIQWLDQANSFCSTLVDRIVTGYPRDEVAKLEEELGYHDGFLDTAEHFYLFVIQGPKS 254
           +AF  WLD A +FCSTLVDRIVTGYPR E+A +E+ELGY D FL TAE+FYLFVI+GP  
Sbjct: 193 DAFNGWLDSACTFCSTLVDRIVTGYPRGEIAAIEKELGYTDAFLVTAEYFYLFVIEGPAW 252

Query: 255 LATELRLDKYPLNVLIVDDIKPYKERKVAILNGAHTALVPVAFQAGLDTVGEAMNDAEIC 314
           LA EL+L    LN+ +VDDI PYK+RKV +LNG HT++VPVA  AGL+TVG AM+D  + 
Sbjct: 253 LADELKLAGADLNIQLVDDITPYKQRKVGVLNGGHTSMVPVALLAGLETVGAAMDDPLVS 312

Query: 315 AFVEKAIYEEIIPVLDLPRDELESFASAVTGRFRNPYIKHQLLSIALNGMTKFRTRILPQ 374
            F+ + + EEIIP L LPR EL+ FA+ V  RFRNPYI+H+L SIALN  +KF  R++PQ
Sbjct: 313 RFLLRTLDEEIIPALPLPRAELDPFAADVLLRFRNPYIQHRLESIALNSWSKFAARVMPQ 372

Query: 375 LLAGQKANGTLPARLTFALAALIAFYRGERNGETYPVQDDAHWLERYQQLWSQHRDRVIG 434
           LL  QK NG LP RL FALAA +  YR    G    + DD   L  ++  W + R   I 
Sbjct: 373 LLQYQKTNGVLPQRLVFALAANMLLYR----GLMVTLTDDPAHLAWFEDAWEKFRTHRIN 428

Query: 435 TQELVAIVLAEKDHWEQDLTQVPGLVEQVANDLDAILEKGMREAVRPL 482
             E+    LA K  W  DL QVP L E +   L  I   G+R+A+  L
Sbjct: 429 FAEIAQGWLANKAVWGADLNQVPQLTESLEKTLQLIDINGVRKALLEL 476


Lambda     K      H
   0.321    0.138    0.413 

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: 701
Number of extensions: 31
Number of successful extensions: 2
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: 483
Length of database: 477
Length adjustment: 34
Effective length of query: 449
Effective length of database: 443
Effective search space:   198907
Effective search space used:   198907
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 51 (24.3 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