Alignments for a candidate for xylK_Tm in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylK_Tm in Phaeobacter inhibens BS107

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF385 PGA1_c03960 ribose import ATP-binding protein RbsA

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__Phaeo:GFF385
          Length = 509

 Score =  283 bits (724), Expect = 1e-80
 Identities = 169/492 (34%), Positives = 270/492 (54%), Gaps = 31/492 (6%)

Query: 15  LKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVN 74
           ++ KGI K F  V A  ++   V    I  +IGENGAGKSTL+ IL G  K D GE+ ++
Sbjct: 6   IELKGISKAFGPVQANKDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGEVWIH 65

Query: 75  GERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMY 134
           G+R E      A   GI ++ Q   L +N TV ENI L  E     K +LS         
Sbjct: 66  GKRTEIPDSQAAISAGIGMVFQHFKLVENFTVLENIILGAEDGGLLKPSLSKA------- 118

Query: 135 TRSKELLDLIGA---KFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEE 191
              K L DL         PDA +  +    +Q VEI KAL ++  I+ +DEPT  LT  E
Sbjct: 119 --RKSLKDLAAEYELNVDPDARIDEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAE 176

Query: 192 TERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKM 251
            ++LF I++ L++ G +++ ++H+L E+M  +D + VMR G+    +K  E   + + ++
Sbjct: 177 ADQLFRILDRLRAEGKTIILITHKLREIMEYTDTVSVMRRGEMTATVKTAETSPEHLAEL 236

Query: 252 MVGREVEFFPHGIETRPGEIALEVRNLKWKD-----KVKNVSFEVRKGEVLGFAGLVGAG 306
           MVGR+V      +   PG+  LE+ NL   D     +VKN+   VR GE+LG AG+ G G
Sbjct: 237 MVGRKVLLRVDKVPATPGKPILEIENLSVVDEAGVARVKNIDLTVRAGEILGIAGVAGNG 296

Query: 307 RTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMG----IGLIPEDRKLQGLVLRMT 362
           ++E M ++ G+ + + G I +NG  + +       +      +  +PEDR+ +GL++   
Sbjct: 297 QSELMEVLGGMREGQ-GSIRLNGAPLPLSGAGSDARARRAAHVAHVPEDRQREGLIMDFH 355

Query: 363 VKDNIVL-----PSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQ 417
             +N+       P  ++    GL+++       +E  + +  ++ P  +   +N SGGNQ
Sbjct: 356 AWENVAFGYHHAPEYQR----GLLMNNAALRADTEAKMAKFDVRPPDPWLAAKNFSGGNQ 411

Query: 418 QKVVLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNL 477
           QK+V+A+ +  N ++L+  +PTRG+D+GA   IH+ I EL  QGKA++++S EL EIL+L
Sbjct: 412 QKIVVAREIERNPELLLIGQPTRGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSL 471

Query: 478 SDRIVVMWEGEI 489
           +DR+ VM++G I
Sbjct: 472 ADRVAVMFDGMI 483



 Score =  106 bits (264), Expect = 2e-27
 Identities = 70/222 (31%), Positives = 118/222 (53%), Gaps = 25/222 (11%)

Query: 285 KNVSFEVRKGEVLGFAGLVGAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMG 344
           K++S  V  G + G  G  GAG++  M +++G  + + G+++++G++ EI + + AI  G
Sbjct: 22  KDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGEVWIHGKRTEIPDSQAAISAG 81

Query: 345 IGLIPEDRKLQGLVLRMTVKDNIVL---------PSLKKISRWGLVLDERKEEEISEDYV 395
           IG++ +  KL   V   TV +NI+L         PSL K  +   + D   E E++ D  
Sbjct: 82  IGMVFQHFKL---VENFTVLENIILGAEDGGLLKPSLSKARK--SLKDLAAEYELNVDPD 136

Query: 396 KRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIR 455
            R+           + +  G QQ+V + K L   ADILI DEPT  +      ++ R++ 
Sbjct: 137 ARI-----------DEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEADQLFRILD 185

Query: 456 ELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAVLDNRE 497
            L A+GK +I+I+ +L EI+  +D + VM  GE+TA +   E
Sbjct: 186 RLRAEGKTIILITHKLREIMEYTDTVSVMRRGEMTATVKTAE 227



 Score = 71.6 bits (174), Expect = 6e-17
 Identities = 60/241 (24%), Positives = 108/241 (44%), Gaps = 19/241 (7%)

Query: 26  GVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSP-V 84
           GV  V N+D  V   EI+ + G  G G+S L+++L G ++   G I +NG  +       
Sbjct: 270 GVARVKNIDLTVRAGEILGIAGVAGNGQSELMEVLGG-MREGQGSIRLNGAPLPLSGAGS 328

Query: 85  DA-FKKGISVIH-----QELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSK 138
           DA  ++   V H     Q   L  +    EN+   Y      +R L          T +K
Sbjct: 329 DARARRAAHVAHVPEDRQREGLIMDFHAWENVAFGYHHAPEYQRGLLMNNAALRADTEAK 388

Query: 139 ELLDLIGAKFS-----PDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193
                  AKF      P    +N +   +Q + + + + + P ++ + +PT  + +   E
Sbjct: 389 M------AKFDVRPPDPWLAAKNFSGGNQQKIVVAREIERNPELLLIGQPTRGVDIGAIE 442

Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253
            + + I  L+ +G +++ VS  L+E++ ++DR+ VM DG  +GE    + D   +  +M 
Sbjct: 443 FIHKQIVELRDQGKAILLVSVELEEILSLADRVAVMFDGMIMGERPADQTDEKELGLLMA 502

Query: 254 G 254
           G
Sbjct: 503 G 503


Lambda     K      H
   0.319    0.138    0.381 

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: 685
Number of extensions: 37
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 520
Length of database: 509
Length adjustment: 35
Effective length of query: 485
Effective length of database: 474
Effective search space:   229890
Effective search space used:   229890
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

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

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources