GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00885 in Dinoroseobacter shibae DFL-12

Align ABC-type branched-chain amino acid transport system, permease component protein (characterized, see rationale)
to candidate 3607448 Dshi_0861 inner-membrane translocator (RefSeq)

Query= uniprot:D8IUY4
         (309 letters)



>FitnessBrowser__Dino:3607448
          Length = 305

 Score =  132 bits (331), Expect = 1e-35
 Identities = 93/312 (29%), Positives = 152/312 (48%), Gaps = 23/312 (7%)

Query: 3   IFIQQIINGLVLGSMYALIALGYTMVYGVLNLINFAHGDILMVGAMVGLSLLKVVQQVAP 62
           + I+Q++NGL  G M  L+A G T+V+GV+ LIN AHG + MVGA    ++         
Sbjct: 5   LLIEQVLNGLQFGVMLFLMAAGLTLVFGVMGLINLAHGSLYMVGAFAAAAV--------A 56

Query: 63  GLPGIVQLVIAIVGAIPVCIVVSLLIERIAYRPLRNAPRLAPLITAIGVSILLQTLAMMI 122
           G  G    V+ +  A+        LIE    R L     L  ++    + ++       I
Sbjct: 57  GATG--SFVLGLAAALAAAAAAGALIEVTIIRRLYARDHLDQVLATFALILIFSEGTRWI 114

Query: 123 WGRSP--LPFPQVMPSDPVHIAGALISPT-QIMLLALAVLAMVGLVLIVEKTKMGRAMRA 179
           +G  P  L  P  + S PV +   +  P  ++ ++ + +     L  ++ KT++G  +RA
Sbjct: 115 FGSFPLFLEVPAAL-SGPVTLPFGIEYPAYRLAIIGIGLAIAAALFWLIAKTRIGVQIRA 173

Query: 180 TAENPRIAGLMGVDANKVIVVTFAIGAGLAAIAGVMWAANYSTAQFAMGFVPGLKAFSAA 239
              +  +   +GVD +++  + FA+GA LA +AG +  A   + Q  MG    + AF   
Sbjct: 174 GEADREMIAALGVDIDRLYTLVFALGAALAGLAGALVGA-LQSVQVGMGEPVLILAFVVI 232

Query: 240 VLGGIGNIYGAMLGGILLGLIESLGAGYIGDLTGNFL--------GSNYQDIFAFIVLII 291
           V+GGIG+I GA +G +LLGL ++LG   +    G  L        GS    +  +I++  
Sbjct: 233 VIGGIGSIKGAFVGALLLGLTDTLGRTLLPVAFGTVLEPSMATAVGSALASMAIYILMAG 292

Query: 292 VLTLRPSGIMGE 303
           VL  RPSG+ G+
Sbjct: 293 VLIFRPSGLFGQ 304


Lambda     K      H
   0.328    0.144    0.416 

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: 234
Number of extensions: 8
Number of successful extensions: 4
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: 309
Length of database: 305
Length adjustment: 27
Effective length of query: 282
Effective length of database: 278
Effective search space:    78396
Effective search space used:    78396
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.

Links

Downloads

Related tools

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