GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Dethiosulfovibrio salsuginis USBA 82

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_085545256.1 B9Y55_RS10130 ABC transporter ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



>NCBI__GCF_900177735.1:WP_085545256.1
          Length = 503

 Score =  152 bits (385), Expect = 1e-41
 Identities = 81/231 (35%), Positives = 141/231 (61%), Gaps = 2/231 (0%)

Query: 7   IRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGK 66
           ++ + KSF  +KA D + + + KGEV+ALLG+NGAGKSTL+ ++SG + PD G +   G 
Sbjct: 1   MKGITKSFQGIKANDQIDLTLKKGEVLALLGENGAGKSTLMNVLSGIYLPDGGTIDIGGT 60

Query: 67  KVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEESKKLLD 126
           ++ F SPNDA S GI  ++Q   L+P   ++ N+ L      +I L K K++ E   +  
Sbjct: 61  RLSFRSPNDAISAGIGMVHQHFMLVPSQTVWENMVLGLPDLPQI-LPKGKIISEITAISK 119

Query: 127 SLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARN 186
              + + D    +  LS G++Q V + + +Y +A+++++DEPTA L+  EAR +    + 
Sbjct: 120 QYGLEV-DPEAIIWQLSIGEQQRVEILKTLYRNAQVLILDEPTAVLTPQEARSLFNTIKR 178

Query: 187 LKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVM 237
           + ++G G++ I+H + +  E++DR+ VL +GK+I    +E  + E+I E+M
Sbjct: 179 MTEEGRGIIFISHKLDEVMEISDRVTVLRKGKLIGTVDRENASKEKIAEMM 229



 Score = 97.4 bits (241), Expect = 5e-25
 Identities = 65/240 (27%), Positives = 123/240 (51%), Gaps = 8/240 (3%)

Query: 17  VKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVFEGKKVIFNSPNDA 76
           +KALD VS+E+ +G+++ L G  G G++ L ++++G  K   G L+ +GK+V  +SP + 
Sbjct: 263 LKALDQVSLELREGQILGLAGVAGNGQTELCQVMAGLRKMTSGKLILKGKEVTDSSPREL 322

Query: 77  RSLGIETIYQD---LALIPDLPIYYNIFLAR----EVTNKIFLNKKKMMEESKKLLDSLQ 129
              GI  I  D     ++ ++ +  N  L R     V   + ++ K +++ +  ++ +  
Sbjct: 323 IDGGIRYIPADRKGTGMVSNMDVRENSTLKRYWRRPVARGVLIDWKAVLKHALGIVKNFN 382

Query: 130 IRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVLELARNLKK 189
           +  P +   V NLSGG  Q + + R +    K+++   PT  L V   R V E     ++
Sbjct: 383 VDTPSVETPVRNLSGGNIQKLMLGRELSDIPKVLIAMNPTWGLDVAATRFVREQLLEERE 442

Query: 190 KGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEET-NVEEITEVMTSFALGKVNLG 248
           KG  + +I+ ++ +   ++DRI V+ RGKI+   +   T  +E I  +M    + +V  G
Sbjct: 443 KGAAIFLISEDLDELMSLSDRIAVMYRGKIMGLVEDPNTFGIERIGMMMAGTRIEQVGGG 502


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: 278
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: 503
Length adjustment: 29
Effective length of query: 222
Effective length of database: 474
Effective search space:   105228
Effective search space used:   105228
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