GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Dshi_0548 in Phaeobacter inhibens BS107

Align ABC transporter for Xylitol, permease component 1 (characterized)
to candidate GFF1647 PGA1_c16700 binding protein-dependent transport system, inner membrane component

Query= reanno::Dino:3607126
         (288 letters)



>FitnessBrowser__Phaeo:GFF1647
          Length = 316

 Score =  137 bits (346), Expect = 2e-37
 Identities = 87/276 (31%), Positives = 135/276 (48%), Gaps = 7/276 (2%)

Query: 11  FAFIGPAVIGLALVGIAPLLYALWTSLHFYNLTKLRRVEFIGLENYWTVLTDEVFWQAMG 70
           F ++ P ++ +  V + PL+  +  S     L       ++G ENY  + +D  FW A+ 
Sbjct: 34  FLYLSPMILLIGSVMLIPLIVGISYSFQSIELLNPFATGWVGFENYEKLWSDRKFWIALE 93

Query: 71  RTFFLLGTALPLQIALGLGIALVLHQPGLTLVKTLARLSLVLPMATTYAVVGLLGQVMFN 130
            TFF    ++  Q  LGLG+A++L+       K L +  + LP A    +  L    +FN
Sbjct: 94  NTFFWTFWSIFFQFFLGLGLAMLLNTQFFG--KKLFQALVFLPWAVPTFLSALTWAWLFN 151

Query: 131 QKFGVVNQLLGGADI-----NWIGDPENAFAMIIFWDVWQWTPFVALVLLAGLTMVPGEV 185
              G +   L    +     N +GDP+ A    I  ++W   PF A+ LLA L  +PGE+
Sbjct: 152 PVIGPIPHWLAALGVLSEPYNILGDPDLAIWGPITANIWFGVPFFAITLLAALQSIPGEL 211

Query: 186 EEAARLETKSKWTVLRYVQLPFLLPGLVAVLILRTADTLKLFDMVFTLTRGGPGSSTEFI 245
            EAA ++  + W     + LPFL P +   ++LRT       D++F +T GGP +ST+ +
Sbjct: 212 YEAAEIDGATPWQSFTKITLPFLAPMIAITVMLRTIWIANFADLIFVMTGGGPANSTQIL 271

Query: 246 SLMIQRVGFRGFDQGLASAQAIILLIITIVLAQIYI 281
           S  I    FR  D G AS  A+ LLII +  A I +
Sbjct: 272 STYIFTTAFRKLDFGYASTIAVALLIILLAYAVILL 307


Lambda     K      H
   0.329    0.144    0.440 

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: 313
Number of extensions: 13
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: 288
Length of database: 316
Length adjustment: 27
Effective length of query: 261
Effective length of database: 289
Effective search space:    75429
Effective search space used:    75429
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 (21.8 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