GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylGsa in Pseudomonas simiae WCS417

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



>lcl|FitnessBrowser__WCS417:GFF2332 PS417_11890 D-ribose transporter
           ATP-binding protein
          Length = 517

 Score =  160 bits (405), Expect = 5e-44
 Identities = 87/243 (35%), Positives = 149/243 (61%), Gaps = 2/243 (0%)

Query: 4   LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63
           LLEI ++ K F  V AL  V + +  G V+AL+G+NGAGKSTL+KII+G ++PD G++  
Sbjct: 23  LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82

Query: 64  EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKI-FLNKKKMMEESK 122
            GK ++F +P  A+  GI  I+Q+L L+P + I  NI++ RE  N +  +N ++M   + 
Sbjct: 83  RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142

Query: 123 KLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLE 182
           +LL  L+I + D   +V NLS  +RQ V +A+AV + + +++MDEPT+A++  E   +  
Sbjct: 143 ELLARLRINL-DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201

Query: 183 LARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTSFAL 242
           +  +LK +G G++ ITH + + + +AD + V   G  I  ++ +  N + +  +M    L
Sbjct: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261

Query: 243 GKV 245
            ++
Sbjct: 262 SQL 264



 Score = 91.7 bits (226), Expect = 3e-23
 Identities = 57/242 (23%), Positives = 121/242 (50%), Gaps = 17/242 (7%)

Query: 4   LLEIRDVHKSFGAVKALDGV----SMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRG 59
           LL +RD+         LDGV    S +++ GE++ + G  G+G++ + + I G      G
Sbjct: 276 LLTVRDL--------TLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSG 327

Query: 60  DLVFEGKKVIFNSPNDARSLGIETIYQDL---ALIPDLPIYYNIFLA--REVTNKIFLNK 114
            +  +GK V  + P+ A   G   + +D     L P L +  N+ +A     T   F+ +
Sbjct: 328 QITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQ 387

Query: 115 KKMMEESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSV 174
           K +    + +   L+++ P +   ++ LSGG +Q   +AR +  + +++++DEPT  + V
Sbjct: 388 KALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDV 447

Query: 175 VEARKVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEIT 234
               ++  L   L  +G+ V++I+  + +   ++DR+ V+  G+++    + E   E++ 
Sbjct: 448 GAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVM 507

Query: 235 EV 236
           ++
Sbjct: 508 QL 509


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: 242
Number of extensions: 10
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: 517
Length adjustment: 29
Effective length of query: 222
Effective length of database: 488
Effective search space:   108336
Effective search space used:   108336
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, 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