GapMind for catabolism of small carbon sources

 

Alignments for a candidate for malF_Aa in Dyella japonica UNC79MFTsu3.2

Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate N515DRAFT_3134 N515DRAFT_3134 multiple sugar transport system permease protein

Query= uniprot:C8WUR0
         (321 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3134
          Length = 292

 Score =  130 bits (328), Expect = 3e-35
 Identities = 91/291 (31%), Positives = 146/291 (50%), Gaps = 16/291 (5%)

Query: 24  AYGYLSPALVTICVLSILPIFYTIYISFTNFNQMHFLSYQ---FVGLKNYEELLNPHDPL 80
           A+ +L+PAL+ + +  +LP+   + +S T+++       +   FV L NY ELL  H PL
Sbjct: 7   AWLFLAPALLVLGLFFLLPVIAALALSLTDYDLYALADIRDLRFVALGNYWELL--HRPL 64

Query: 81  SNLFLPTFIWTLVYALCTTALAYLVGLFLAVLLNNKHMRERTLYRTLLIVPWAVPNLISM 140
              F      TL + L    L+ +  L  A+LLN+   R + L+RT L  P     +   
Sbjct: 65  ---FWSALGHTLYFVLVGVPLSIVASLGAALLLNSPLARCKPLFRTALFAPVVTTVVAVA 121

Query: 141 LAWQGLLNDQYGQINALLHGVFGLPRIPWLTSALWARIAVIMVNVWAGFPYMMTVCLGAL 200
           + W+ L N +YG  N  L G+ G+  + WL    WA   +I+  VW  F Y M + L AL
Sbjct: 122 VIWRYLFNTKYGLANYALGGL-GIHPVDWLGDPRWAMPTIILFAVWKNFGYNMIIFLAAL 180

Query: 201 QSIPTDQYEAAEIDGANWWQVFRYVTMPSVWRISLPLLIPSFSYNFNNFNASYLLTGGGP 260
           Q+IP D YEAA IDGA+  + FR++T+P +    L + I + S  F  F   +++T GGP
Sbjct: 181 QAIPADLYEAARIDGASPLRQFRHITLPMLGPTLLMVGILTVSGYFQLFAEPFVMTEGGP 240

Query: 261 PNSNNPFLGQTDILATAAYKMTLTFNRYDLGATISVLLFILVALISWVQMR 311
                  L  T  +    Y+    +      + ++ LLF+++  ++ V +R
Sbjct: 241 -------LQSTTSVLYLMYEEGFKWWNLGSASAVAFLLFLIMFAVTAVMLR 284


Lambda     K      H
   0.327    0.140    0.451 

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: 311
Number of extensions: 21
Number of successful extensions: 3
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: 321
Length of database: 292
Length adjustment: 27
Effective length of query: 294
Effective length of database: 265
Effective search space:    77910
Effective search space used:    77910
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 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