GapMind for catabolism of small carbon sources

 

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

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 3607445 Dshi_0858 ABC transporter related (RefSeq)

Query= uniprot:Q1MCU3
         (247 letters)



>FitnessBrowser__Dino:3607445
          Length = 230

 Score =  166 bits (421), Expect = 3e-46
 Identities = 94/218 (43%), Positives = 133/218 (61%), Gaps = 5/218 (2%)

Query: 10  PLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSVV 69
           PL+Q+ GV   YG  +AL GVD+ + +G  ++L+G NG GKST + T+CG      G V 
Sbjct: 3   PLVQIEGVTAAYGASQALFGVDLTLKEGGALALMGRNGMGKSTTLKTLCGLLPPTGGRVR 62

Query: 70  FEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLKHFAEDVEKIFTL 129
             G +IT  P H IARL +   PEGRR F  +TV ENL   A     +    D+ ++  L
Sbjct: 63  LAGVEITGRPAHRIARLGVGLVPEGRRCFAPLTVAENLLAAA-----RPGPWDMARVGAL 117

Query: 130 FPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIRKL 189
           FPRL ER  Q   +LSGGEQQML+IGRALM  P+LL+LDE + GLAP++ + I+ AI +L
Sbjct: 118 FPRLAERRDQVARSLSGGEQQMLAIGRALMTNPRLLVLDEATEGLAPVVRQEIWAAIARL 177

Query: 190 NEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGS 227
               GL++ LV+++     +++  A ++  G+   SGS
Sbjct: 178 RAEGGLSLILVDKSLRELRQVADTAVILARGRTVWSGS 215


Lambda     K      H
   0.320    0.137    0.387 

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: 185
Number of extensions: 7
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: 247
Length of database: 230
Length adjustment: 23
Effective length of query: 224
Effective length of database: 207
Effective search space:    46368
Effective search space used:    46368
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: 46 (22.3 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