GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylB in Pseudomonas simiae WCS417

Align Xylulose kinase; Xylulokinase; EC 2.7.1.17 (uncharacterized)
to candidate GFF3460 PS417_17715 actin

Query= curated2:Q9CFG8
         (501 letters)



>FitnessBrowser__WCS417:GFF3460
          Length = 510

 Score =  231 bits (590), Expect = 4e-65
 Identities = 154/511 (30%), Positives = 260/511 (50%), Gaps = 21/511 (4%)

Query: 1   MTYVLGIDLGTSSLKGILMDEVGNLITTKSAEYQIDTPKQGYSEQRPEYWIVALESVLTG 60
           M YV+G+D+GT S K +L+D  G +I   S  Y++DTPK  ++EQ P+ W+ A+E+ +  
Sbjct: 1   MNYVMGVDIGTQSTKALLVDGQGTIIAQHSQGYRVDTPKVRWAEQWPQVWLDAVEACVAQ 60

Query: 61  LSVEISDFGQQLAGISFSGQMH-SLVVLDDNNKPVYPAILWNDVRTSKQCQEITDRLG-Q 118
              +     +Q+  +  S     S + +D    P++P ++W D R  +Q   + +++   
Sbjct: 61  CMAKAGVAAEQVKALCISSLYGGSGIAVDAQITPLHPCLIWMDRRAGEQVAWVREQVDLD 120

Query: 119 RLLEITKNIALEGFTLPKILWLQENEPEVWSRVKKIMLPKDYLSLWLTGNIYTEFSDAAG 178
           RL  IT N     +   K+LWL++++PEVW+  + ++ P  Y++  LTG +  + S +AG
Sbjct: 121 RLFAITGNSVDSYYGFTKMLWLKQHQPEVWANTRYLLPPNSYINWCLTGELAVDHS-SAG 179

Query: 179 TL--LLDIEKKQWSEEITDAFNIDRRILPE-LIESTDRTGFVKAEIAERYKLTNEVKVFA 235
            +  + D++ + WS E+ DA  I + ++P+ L+ S +  G +    A R  L     + A
Sbjct: 180 NIGGVYDVKARDWSGEMLDALGIPQTMMPQRLVYSGEVVGGLLDTWATRLGLQAGTPLLA 239

Query: 236 GGADNAAAALGVGLINEEVGLISMGTSGVVSAYEPKIADYKGKLHFFNHTVPGA--CYSM 293
           GG D A A L  G+      +  +GTS        ++  + G L    H   G    Y  
Sbjct: 240 GGVDAAMATLAAGVTQPGNHVAMIGTSMCWGYLNQQVDAHHG-LVSMPHVYNGHRDLYIF 298

Query: 294 GVTLAAGNSLNWYKETFGKGL----------SFNELLSEVYTVSPGSEGLLFTPYIVGER 343
           G  + AG S++W++E F +            S   L      +  GSEGLLF PY++GER
Sbjct: 299 GGAITAGASVSWFREQFCQAEEQQAKVTGQDSLVLLEQRAMNLPAGSEGLLFLPYLMGER 358

Query: 344 TPHFDSKIRGSFIGISAHHEQKHFSRAVLEGITFSLRDSKDIMEKTKNKKFKRLISVGGG 403
           +P +D +  GSF+G++ +H + H  RAVLEG++F+LR + +   +  +    RLI VGG 
Sbjct: 359 SPVWDDRASGSFVGLNLYHGRIHLYRAVLEGVSFALRHNIEAGTRGAHSLDPRLIVVGGA 418

Query: 404 AQNPDIMQMQADIFNSEMIRLTVEQGPGLGACMIAAFGCGLFDSLEAVTKAFVHYKEASF 463
           + +   MQ+ ADI    +  +  E    LGA ++AA   GL    E + K +V     + 
Sbjct: 419 SHSDLWMQIIADITQYPVYTIVQEVEAALGAALLAAHSVGLVSDGE-MDKGWVQLALRA- 476

Query: 464 IPNPKNVARYEQIYQIWKQVYKNTSEISHQL 494
            P  +NV  Y++ +  + ++Y     I H L
Sbjct: 477 EPKVENVGVYDRAFAEYLKLYPALKPIMHNL 507


Lambda     K      H
   0.317    0.135    0.394 

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: 612
Number of extensions: 23
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 501
Length of database: 510
Length adjustment: 34
Effective length of query: 467
Effective length of database: 476
Effective search space:   222292
Effective search space used:   222292
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 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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