GapMind for catabolism of small carbon sources

 

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

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate N515DRAFT_3232 N515DRAFT_3232 xylose ABC transporter ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3232
          Length = 513

 Score =  144 bits (362), Expect = 5e-39
 Identities = 79/239 (33%), Positives = 140/239 (58%), Gaps = 3/239 (1%)

Query: 2   SDLLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGY--HKPDRG 59
           S L E+R + KSFG VKALDG+ + +  GE + L G+NGAGKSTL+K++SG   H    G
Sbjct: 5   SCLFEMRGIAKSFGGVKALDGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWDG 64

Query: 60  DLVFEGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNK-IFLNKKKMM 118
           +++++G+ +   S  D+   GI  I+Q+L L+P L +  NIFL  E+T     ++   M 
Sbjct: 65  EILWQGQPLRARSVRDSERAGIVIIHQELMLVPQLSVAENIFLGHEITRPGGRMDYDAMY 124

Query: 119 EESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEAR 178
            ++  LL  L +   ++ +   +  GG +Q   +A+A+   AK++++DEPT++L+  E  
Sbjct: 125 AKADALLQELGLHDVNVALPAMHYGGGHQQLFEIAKALAKQAKLLILDEPTSSLTSSETE 184

Query: 179 KVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVM 237
            +L +  +LK++G+  + I+H + +   V D + V+  G+ I  +   E +V+ +  +M
Sbjct: 185 VLLGIVEDLKRRGVACIYISHKLDEVERVCDTVCVIRDGRHIATQPMHELDVDTLITLM 243



 Score = 80.1 bits (196), Expect = 8e-20
 Identities = 49/208 (23%), Positives = 107/208 (51%), Gaps = 6/208 (2%)

Query: 18  KALDGVSMEINKGEVVALLGDNGAGKSTLIKIISG-YHKPDRGDLVFEGKKVIFNSPNDA 76
           K +D VS ++ +GE++ + G  GAG++ L+  I G Y      +L  EG+ +   SP DA
Sbjct: 280 KRVDDVSFQLRRGEILGIAGLVGAGRTELVSAIFGAYTGKSSVELFLEGRPLKIRSPADA 339

Query: 77  RSLGIETIYQDL---ALIPDLPIYYNIFLAR--EVTNKIFLNKKKMMEESKKLLDSLQIR 131
              G+  + +D     ++P L +  NI LA      +   +++++ +   +  +   +++
Sbjct: 340 IRAGLGMVPEDRKRHGIVPLLGVGDNITLATLDHYAHAGHIDRQRELVAIEAQIAERRVK 399

Query: 132 IPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNLKKKG 191
                + +  LSGG +Q   +A+ +    K++++DEPT  + V    ++  L   L  +G
Sbjct: 400 TASPALPIARLSGGNQQKAVLAKMLLARPKVLILDEPTRGVDVGAKAEIYRLIFELAAQG 459

Query: 192 LGVLIITHNIIQGYEVADRIYVLDRGKI 219
           + +++++  + +   +ADR+ V+  G++
Sbjct: 460 VAIVLVSSEMPEVLGMADRVLVMGEGRL 487


Lambda     K      H
   0.318    0.137    0.371 

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: 233
Number of extensions: 10
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 251
Length of database: 513
Length adjustment: 29
Effective length of query: 222
Effective length of database: 484
Effective search space:   107448
Effective search space used:   107448
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 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