GapMind for catabolism of small carbon sources

 

Alignments 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 GFF3463 PS417_17730 ribonucleotide-diphosphate reductase subunit alpha

Query= uniprot:P0DTT6
         (251 letters)



>FitnessBrowser__WCS417:GFF3463
          Length = 502

 Score =  165 bits (418), Expect = 1e-45
 Identities = 86/238 (36%), Positives = 154/238 (64%), Gaps = 2/238 (0%)

Query: 1   MSDLLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGD 60
           MS LL++ ++ K +  V+AL  +++++ +GE+ ALLG+NGAGKSTL+KI+ G    D G 
Sbjct: 1   MSSLLKLENICKRYPGVQALKSINLQVERGEIHALLGENGAGKSTLMKILGGVEHQDEGQ 60

Query: 61  LVFEGKKVIFNSPNDARSLGIETIYQDLALIPDLPIYYNIFLAREVTNKI-FLNKKKMME 119
           ++ +G+   F +  DA + GI  ++Q+ +LIP L    NIFL  E++N+   L K++M+E
Sbjct: 61  ILIDGQAQQFATYRDAIAAGIGIVFQEFSLIPYLTAVENIFLGHELSNRFGLLRKREMVE 120

Query: 120 ESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARK 179
            S+ L   L + I D+   V++LS  ++Q V +A+A+   A+++++DEPTA L+  EA  
Sbjct: 121 ASEALFKRLGVTI-DLQCAVKHLSVAEQQFVEIAKALALDARLLVLDEPTATLTPSEAEL 179

Query: 180 VLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEITEVM 237
           + E+ R LK++G+ V+ I+H++ + ++V DRI VL  G  +      +++++ + E+M
Sbjct: 180 LFEIMRELKRQGVAVIFISHHLEEIFQVCDRISVLRDGGNVGVTDVADSDIDHLVEMM 237



 Score = 82.0 bits (201), Expect = 2e-20
 Identities = 59/236 (25%), Positives = 112/236 (47%), Gaps = 10/236 (4%)

Query: 4   LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63
           LLE++D+      V+       +++KGE++   G  G+G++ L   + G       D+  
Sbjct: 258 LLEVKDIQ----LVRNGPHNRFQLHKGEILGFAGLVGSGRTELALGMMGALPSVSKDVWL 313

Query: 64  EGKKVIFNSPNDARSLGIETIYQDL---ALIPDLPIYYNIFL---AREVTNKIFLNKKKM 117
            G+K+  + P  A + GI  + +      LI D  I  NI L    +       ++K + 
Sbjct: 314 RGEKITLDDPAQALAHGIGLLPESRKSEGLITDFSIRENISLNNLPKYQNASGLIDKNRE 373

Query: 118 MEESKKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEA 177
               + L+  L I+ P    +V NLSGG +Q V +AR +     +++ DEPT  + V   
Sbjct: 374 CASVEGLMKQLSIKAPSSESRVFNLSGGNQQKVVIARWINHHCDVLVFDEPTRGIDVGAK 433

Query: 178 RKVLELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEETNVEEI 233
            ++  L R+L ++G  +++I+  + +   + DR+ V  +G I+   +    N +E+
Sbjct: 434 AQIYALMRSLTEQGYAIIMISSELPEIIGMCDRVAVFHKGAIVKLLEASAVNPQEV 489


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: 258
Number of extensions: 9
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: 502
Length adjustment: 29
Effective length of query: 222
Effective length of database: 473
Effective search space:   105006
Effective search space used:   105006
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 (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