GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Tistlia consotensis USBA 355

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_085124759.1 B9O00_RS21320 sugar ABC transporter ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



>NCBI__GCF_900177295.1:WP_085124759.1
          Length = 518

 Score =  147 bits (370), Expect = 6e-40
 Identities = 80/235 (34%), Positives = 137/235 (58%), Gaps = 1/235 (0%)

Query: 4   LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63
           LLE+R V + F  V ALD V  ++  GEV  L G+NGAGKST+I +I+G  +P  G+  F
Sbjct: 23  LLELRGVSRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSEGEFRF 82

Query: 64  EGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKK 123
            G+ V  NS + AR LGI  ++Q+ +L+P + +  N+FL  E T    L+++ + + +  
Sbjct: 83  RGEPVELNSVHHARGLGISAVFQEFSLVPQMTVEENLFLGAESTRLGLLDRRALHDRADA 142

Query: 124 LLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLEL 183
           +L  L   +   + +V +L+  ++Q V +A+A      ++++DEPTA+L+  E  ++ +L
Sbjct: 143 ILKRLGFPLRPRD-RVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASLTERETAQLFKL 201

Query: 184 ARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVMT 238
              +K +G+GV+ ITH + +   + DRI VL  G+ +     + T   E+  +MT
Sbjct: 202 IEQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELVRLMT 256



 Score = 80.1 bits (196), Expect = 8e-20
 Identities = 61/237 (25%), Positives = 112/237 (47%), Gaps = 12/237 (5%)

Query: 6   EIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEG 65
           E+  V +   A  ++   S+ +  GE+V L G  G+GKS + +   G  K   G +  +G
Sbjct: 274 ELLSVERLTTASGSVVEASLSVCAGEIVGLAGLVGSGKSEVARACFGLEKIAEGHVRLKG 333

Query: 66  KKVIFNSPNDARSLGIETI---YQDLALIPDLPIYYNIFLAREVT----NKIFLNKKKMM 118
           ++V    P      G   +    +D  L+   P+  N+ L         N   L+++   
Sbjct: 334 EEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSLPSLTLAPFGNGALLDRRGET 393

Query: 119 EESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEAR 178
           +  ++L + L ++ P I   VE  SGG +Q V +A++     ++   DEPT  + V    
Sbjct: 394 DRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLAKSRTRPVQVFAFDEPTVGVDVGTRV 453

Query: 179 KVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITE 235
            + E  R+L + G G+L+I+ ++ +   +++R YV  RG++     + E   +EITE
Sbjct: 454 AIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRV-----QAELAGDEITE 505


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: 243
Number of extensions: 12
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: 518
Length adjustment: 29
Effective length of query: 222
Effective length of database: 489
Effective search space:   108558
Effective search space used:   108558
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 Apr 09 2024. 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