GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braG in Dechlorosoma suillum PS

Align ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Dsui_0626 Dsui_0626 ABC-type branched-chain amino acid transport systems, ATPase component

Query= uniprot:Q1MCU3
         (247 letters)



>FitnessBrowser__PS:Dsui_0626
          Length = 238

 Score =  239 bits (609), Expect = 5e-68
 Identities = 123/235 (52%), Positives = 172/235 (73%), Gaps = 2/235 (0%)

Query: 9   QPLLQVNGVETYYGNIRALAGVDVHVNKGEIVSLIGANGAGKSTLMMTICGSPQARTGSV 68
           +PLL V G+   YG I+A+ G+  HV+ GE V+LIGANGAGK++ +  +     A  GSV
Sbjct: 3   EPLLIVEGLRIAYGGIQAVKGITFHVDPGETVALIGANGAGKTSTLKALARQLDAAGGSV 62

Query: 69  VFEGRDITRMPTHEIARLRIAQSPEGRRIFPRMTVLENLQMGAGLDNLK-HFAEDVEKIF 127
            ++GR+I+ +  HE+    IA  PEGR +F R+TV ENL+MGA   + K   A+D+E+IF
Sbjct: 63  RYQGREISALAPHELVGQGIALVPEGRGVFARLTVTENLEMGAYCRHDKAEIADDLERIF 122

Query: 128 TLFPRLKERHAQRGGTLSGGEQQMLSIGRALMARPKLLLLDEPSLGLAPLIVKGIFEAIR 187
            L PRLKERH Q  GTLSGGEQQML++GRALM+RP+LLLLDEPS+GLAP++V+ +FE ++
Sbjct: 123 ALLPRLKERHGQLAGTLSGGEQQMLAMGRALMSRPRLLLLDEPSMGLAPIMVQKVFEVVQ 182

Query: 188 KLNEAEGLTVFLVEQNAFAALRLSHRAYVMVNGKVTMSGSGKELLANPEVRAAYL 242
           ++  ++G+T+ LVEQNA  AL++S R YVM +G +T++ +   LL NP V+AAYL
Sbjct: 183 EV-ASQGMTILLVEQNARLALQVSRRGYVMESGDITLTDAAGTLLDNPRVKAAYL 236


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: 212
Number of extensions: 11
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: 247
Length of database: 238
Length adjustment: 23
Effective length of query: 224
Effective length of database: 215
Effective search space:    48160
Effective search space used:    48160
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