GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylGsa in Shewanella sp. ANA-3

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate 7024900 Shewana3_2074 ABC transporter related (RefSeq)

Query= uniprot:P0DTT6
         (251 letters)



>lcl|FitnessBrowser__ANA3:7024900 Shewana3_2074 ABC transporter
           related (RefSeq)
          Length = 499

 Score =  173 bits (439), Expect = 5e-48
 Identities = 92/242 (38%), Positives = 151/242 (62%), Gaps = 1/242 (0%)

Query: 1   MSDLLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGD 60
           MS +LE++ + K +  VKAL+ VS+ +  GEV ALLG+NGAGKSTL+K+++G    D GD
Sbjct: 1   MSLILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGD 60

Query: 61  LVFEGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEE 120
           ++F G+   FN+P DA+  GI T+YQ++ L+P+L +  N+FL  E      ++ KKM  +
Sbjct: 61  ILFLGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYAD 120

Query: 121 SKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKV 180
           ++ +L   ++ I D++  + + S   +Q +A+AR V  SAK++++DEPTA+L   E + +
Sbjct: 121 ARAVLTQFKLDI-DVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVL 179

Query: 181 LELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTSF 240
             +   LK KG+ ++ ITH + Q Y+++DRI VL  G+ I      E    ++ E M   
Sbjct: 180 FGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGR 239

Query: 241 AL 242
           +L
Sbjct: 240 SL 241



 Score = 89.7 bits (221), Expect = 1e-22
 Identities = 61/217 (28%), Positives = 113/217 (52%), Gaps = 11/217 (5%)

Query: 4   LLEIRDVHKSFGAVK-ALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLV 62
           LL + DV     +VK ++  +++ + KG+ V L G  G+G+S +   + G    D G + 
Sbjct: 262 LLSLEDV-----SVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIH 316

Query: 63  FEGKKVIFNSPNDARSLGIETIYQDL---ALIPDLPIYYNIFLAREVTNKI--FLNKKKM 117
             G+K+  + P DA S GI    +D     +I  L I  NI LA +       +L+  + 
Sbjct: 317 LAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQARIGWWRYLSNTRQ 376

Query: 118 MEESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEA 177
            E ++  +D LQI  PD +  +E LSGG +Q V +AR +     ++++DEPT  + +   
Sbjct: 377 QEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAH 436

Query: 178 RKVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVL 214
            ++++L R L  +G+ +L+ +  + +    ++++ VL
Sbjct: 437 AEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVL 473


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: 244
Number of extensions: 14
Number of successful extensions: 4
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: 499
Length adjustment: 29
Effective length of query: 222
Effective length of database: 470
Effective search space:   104340
Effective search space used:   104340
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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