Alignments for a candidate for xylK_Tm in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylK_Tm in Dinoroseobacter shibae DFL-12

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate 3609459 Dshi_2843 ABC transporter related (RefSeq)

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__Dino:3609459
          Length = 548

 Score =  292 bits (748), Expect = 2e-83
 Identities = 172/489 (35%), Positives = 276/489 (56%), Gaps = 25/489 (5%)

Query: 15  LKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVN 74
           ++ +GI K F  V A  ++   V    I  +IGENGAGKSTL+ IL G  K DAGEI + 
Sbjct: 26  IELRGISKAFGPVQANKDISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADAGEIFIK 85

Query: 75  GERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMY 134
           G++ E      A + GI ++ Q   L +N TV EN+ L  E     + +L+         
Sbjct: 86  GQKTEIPDSQAAIRAGIGMVFQHFKLVENFTVLENVVLGAEEGALLRPSLAKA------R 139

Query: 135 TRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETER 194
              +EL +      +PDAL+ +L+   +Q VEI KAL ++  I+ +DEPT  LT  E + 
Sbjct: 140 KLLRELSEEYELNVAPDALIEDLSVGHQQRVEILKALYRKADILILDEPTGVLTPAEADH 199

Query: 195 LFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVG 254
           LF I+E LK+ G +++ ++H+L E+M  +D + VMR G+    +K  +   + + ++MVG
Sbjct: 200 LFRILEGLKAEGKTIILITHKLREIMETTDTVSVMRRGEMTATVKTADTSPEQLAELMVG 259

Query: 255 REVEFFPHGIETRPGEIALEVRNLKWKD-----KVKNVSFEVRKGEVLGFAGLVGAGRTE 309
           R+V         +PG   L V +L+  D     +VK +S +VR GEVLG AG+ G G++E
Sbjct: 260 RKVLLRVDKTPAQPGAPILTVDDLRVVDDQGVERVKGISLQVRAGEVLGIAGVAGNGQSE 319

Query: 310 TMLLVFGVNQKESGDIYVNGRKVEI----KNPEDAIKMGIGLIPEDRKLQGLVLRMTVKD 365
            +L V G  +  +G + V+G+++++     N +     GI  +PEDR+ +GL++     +
Sbjct: 320 -LLEVLGGMRPATGRVTVSGQQIDLTGKHSNGKTRRAQGIAHVPEDRQAEGLIMDYHAWE 378

Query: 366 NIVL-----PSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKV 420
           N+       P+  +    GL++D R     +E  + R  ++    +   +N SGGNQQK+
Sbjct: 379 NVAFGYHDDPAYNR----GLLMDNRAVRADAEGKIARFDVRPADCWLAAKNFSGGNQQKI 434

Query: 421 VLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDR 480
           VLA+ +  N ++L+  +PTRG+D+GA   IH+ I  L   GKA++++S EL EIL+LSDR
Sbjct: 435 VLAREIERNPELLLVGQPTRGVDIGAIEFIHQQIIALRDAGKAILLVSVELEEILSLSDR 494

Query: 481 IVVMWEGEI 489
           + VM++G I
Sbjct: 495 VAVMFDGRI 503



 Score =  115 bits (288), Expect = 4e-30
 Identities = 75/230 (32%), Positives = 131/230 (56%), Gaps = 11/230 (4%)

Query: 285 KNVSFEVRKGEVLGFAGLVGAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMG 344
           K++S  V  G + G  G  GAG++  M +++G  + ++G+I++ G+K EI + + AI+ G
Sbjct: 42  KDISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADAGEIFIKGQKTEIPDSQAAIRAG 101

Query: 345 IGLIPEDRKLQGLVLRMTVKDNIVLPSLK-KISRWGLVLDERKEEEISEDYVKRLSIKTP 403
           IG++ +  KL   V   TV +N+VL + +  + R  L    +   E+SE+Y   L++   
Sbjct: 102 IGMVFQHFKL---VENFTVLENVVLGAEEGALLRPSLAKARKLLRELSEEY--ELNVAPD 156

Query: 404 SIYQITENLSGGNQQKVVLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKA 463
           ++    E+LS G+QQ+V + K L   ADILI DEPT  +       + R++  L A+GK 
Sbjct: 157 ALI---EDLSVGHQQRVEILKALYRKADILILDEPTGVLTPAEADHLFRILEGLKAEGKT 213

Query: 464 VIMISSELPEILNLSDRIVVMWEGEITAVLDNREKRVTQEEIMYYASGQK 513
           +I+I+ +L EI+  +D + VM  GE+TA +   +   + E++     G+K
Sbjct: 214 IILITHKLREIMETTDTVSVMRRGEMTATVKTAD--TSPEQLAELMVGRK 261



 Score = 70.5 bits (171), Expect = 2e-16
 Identities = 53/237 (22%), Positives = 112/237 (47%), Gaps = 11/237 (4%)

Query: 26  GVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVD 85
           GV  V  +  +V   E++ + G  G G+S L+++L G ++P  G + V+G++++      
Sbjct: 290 GVERVKGISLQVRAGEVLGIAGVAGNGQSELLEVLGG-MRPATGRVTVSGQQIDLTGKHS 348

Query: 86  AFK----KGISVI---HQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSK 138
             K    +GI+ +    Q   L  +    EN+   Y       R L   +D   +   ++
Sbjct: 349 NGKTRRAQGIAHVPEDRQAEGLIMDYHAWENVAFGYHDDPAYNRGLL--MDNRAVRADAE 406

Query: 139 ELLDLIGAKFSPDALV-RNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFE 197
             +     + +   L  +N +   +Q + + + + + P ++ + +PT  + +   E + +
Sbjct: 407 GKIARFDVRPADCWLAAKNFSGGNQQKIVLAREIERNPELLLVGQPTRGVDIGAIEFIHQ 466

Query: 198 IIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVG 254
            I  L+  G +++ VS  L+E++ +SDR+ VM DG+ +GE    E +   +  +M G
Sbjct: 467 QIIALRDAGKAILLVSVELEEILSLSDRVAVMFDGRIMGERPAAETNEKELGLLMAG 523


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: 741
Number of extensions: 33
Number of successful extensions: 8
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: 548
Length adjustment: 35
Effective length of query: 485
Effective length of database: 513
Effective search space:   248805
Effective search space used:   248805
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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Rules (tab-delimited)
Protein sequences (fasta format)
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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