GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Photobacterium gaetbulicola Gung47

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_039469450.1 H744_RS03175 sugar ABC transporter ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



>NCBI__GCF_000940995.1:WP_039469450.1
          Length = 497

 Score =  152 bits (383), Expect = 2e-41
 Identities = 85/244 (34%), Positives = 150/244 (61%), Gaps = 3/244 (1%)

Query: 4   LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63
           +LE+R + K+F  VKALD V + + KG V+AL+G+NGAGKSTL+K++ G ++ D G + +
Sbjct: 5   ILEMRGITKTFPGVKALDNVQLTLKKGRVMALMGENGAGKSTLMKVLFGTYQRDEGTIRY 64

Query: 64  EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLARE-VTNKI-FLNKKKMMEES 121
           +G+ V F+   ++   GI  I+Q+L+ +    I  NI+L RE +T  +  ++ KKM  ++
Sbjct: 65  QGELVDFSGAKESLESGISMIHQELSPVLHRNIAENIWLGREPLTGPLRLIDHKKMFADT 124

Query: 122 KKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVL 181
           + LL  L + + D    + +L+    Q V +A+A+ F +K+I+MDEPT+AL+  E   + 
Sbjct: 125 EALLQRLDLDL-DPRTLMSDLTVATMQMVEIAKAISFESKIIIMDEPTSALTDKEVAHLF 183

Query: 182 ELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTSFA 241
           E+   LK +G+ ++ I+H + + +++ D I V   G  I  ++  +TN +E+ ++M    
Sbjct: 184 EIIEKLKSQGVAMVYISHKMDEIFKICDDITVFRDGCYIGEREARDTNHDELVQMMVGRD 243

Query: 242 LGKV 245
           LG V
Sbjct: 244 LGDV 247



 Score = 87.4 bits (215), Expect = 5e-22
 Identities = 59/227 (25%), Positives = 118/227 (51%), Gaps = 11/227 (4%)

Query: 23  VSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFNSPNDARSLGIE 82
           V+ ++++GE++ + G  GAG++ LI+ + G  + + G++   G++V   +P DA S  + 
Sbjct: 274 VNFKLHEGEILGIAGLVGAGRTELIETLFGVREKETGEIWINGEEVEIKAPQDAISHKMA 333

Query: 83  TIYQDL---ALIPDLPIYYNIFLAREVTNKI----FLNKKKMMEESKKLLDSLQIRIPDI 135
            + +D     L   L I+ N  +A     K      L+ ++M  +S++    L+++ P +
Sbjct: 334 FLTEDRRHSGLYLMLDIFANTSIAHLDAYKSRVANVLDVRQMRSDSEEHCKKLKVKTPHM 393

Query: 136 NMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNLKKKGLGVL 195
           +  ++NLSGG +Q V +AR +     ++ +DEPT  + V    ++ +L R L   G  ++
Sbjct: 394 SEAIDNLSGGNQQKVLLARWMLTKPDILFLDEPTRGIDVGAKSEIYKLMRLLTGMGKSLV 453

Query: 196 IITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMTSFAL 242
           +I+  + +   ++DR+ V+  G +    K E    E   E + S AL
Sbjct: 454 MISSELPEVIGMSDRVLVMHEGNL----KGELDGTEATQEKIMSMAL 496


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: 251
Number of extensions: 7
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: 497
Length adjustment: 29
Effective length of query: 222
Effective length of database: 468
Effective search space:   103896
Effective search space used:   103896
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 24 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