Alignments for a candidate for xylK_Tm in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylK_Tm in Dyella japonica UNC79MFTsu3.2

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2413
          Length = 505

 Score =  345 bits (884), Expect = 3e-99
 Identities = 191/480 (39%), Positives = 293/480 (61%), Gaps = 10/480 (2%)

Query: 11  RMEILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGE 70
           R  +L+A+G+ KRF   +A+D VD  +   E+ +L+G+NGAGKSTLIK+LTGV +PD G 
Sbjct: 9   RPVVLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGS 68

Query: 71  ILVNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDE 130
           + ++G  +   +P++A + GI  ++QE+NLC N++VAEN++    A R  +R     +D 
Sbjct: 69  VELDGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLY----AGRYPRRRRLRMIDW 124

Query: 131 NYMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVE 190
             +   ++ LL  +  +   DA + +   A RQMV I +AL    R++ +DEPTSSL   
Sbjct: 125 RQVRDGARSLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEG 184

Query: 191 ETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIK 250
           E   LF +I  L+ RG++++FV+H LD+V  +SDRI V+RDG R+GE    +     ++ 
Sbjct: 185 EVRELFRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALVN 244

Query: 251 MMVGREVEFFPHGIETR----PGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAG 306
            MVGR++         R        A++ + L  + K+  V  +VR+GE+LG  GL+G+G
Sbjct: 245 AMVGRDLPTVAGADAERAPPPDAPPAIDAQGLGCRGKLHPVDLQVRRGEMLGLGGLLGSG 304

Query: 307 RTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDN 366
           RTE   L+FG+++ E G++ + G +VE+K+P DA+  G+ L PE+RK  G+V  ++V++N
Sbjct: 305 RTELARLLFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAELSVREN 364

Query: 367 IVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWL 426
           IVL +L+    W   +   +++E++   V+ L IK   I      LSGGNQQKV+LA+WL
Sbjct: 365 IVL-ALQARQGW-RGMSRARQDELARQLVQALGIKAADIETPVGLLSGGNQQKVMLARWL 422

Query: 427 ATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWE 486
            T   +LI DEPTRGIDV AK E+   +   A  G AV+ IS+E  E+    DRI VM E
Sbjct: 423 VTEPRLLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWCDRIAVMRE 482



 Score =  111 bits (277), Expect = 7e-29
 Identities = 70/226 (30%), Positives = 124/226 (54%), Gaps = 10/226 (4%)

Query: 33  VDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVDAFKKGIS 92
           VD +V   E++ L G  G+G++ L ++L G+ + + GE+ + GERVE   P DA  +G++
Sbjct: 285 VDLQVRRGEMLGLGGLLGSGRTELARLLFGLDRAERGELRIGGERVELKHPADAVVRGLA 344

Query: 93  VIHQELN---LCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKELLDLIGAKFS 149
           +  +E     +   ++V ENI LA +A +G +    +R DE      +++L+  +G K +
Sbjct: 345 LCPEERKTDGIVAELSVRENIVLALQARQGWRGMSRARQDE-----LARQLVQALGIKAA 399

Query: 150 P-DALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKSRGIS 208
             +  V  L+   +Q V + + LV EPR++ +DEPT  + V   + L   +      G++
Sbjct: 400 DIETPVGLLSGGNQQKVMLARWLVTEPRLLILDEPTRGIDVAAKQELMAEVTRRAHAGMA 459

Query: 209 VVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVG 254
           V+F+S    E+ R  DRI VMR+ ++ GEL  G  +   ++ M+ G
Sbjct: 460 VLFISAETGELTRWCDRIAVMRERRKAGELPGGSTEA-RVLAMIAG 504



 Score = 80.9 bits (198), Expect = 1e-19
 Identities = 53/201 (26%), Positives = 105/201 (52%), Gaps = 5/201 (2%)

Query: 287 VSFEVRKGEVLGFAGLVGAGRTETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIG 346
           V   +R GEV    G  GAG++  + L+ GV + + G + ++GR +    P +A + GIG
Sbjct: 31  VDLALRAGEVHALMGQNGAGKSTLIKLLTGVERPDRGSVELDGRVIAPSTPMEAQRDGIG 90

Query: 347 LIPEDRKLQGLVLRMTVKDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIY 406
            + ++     L   ++V +N+      +  R  ++ D R+  + +   +++L ++   + 
Sbjct: 91  TVYQE---VNLCPNLSVAENLYAGRYPRRRRLRMI-DWRQVRDGARSLLRQLHLEL-DVD 145

Query: 407 QITENLSGGNQQKVVLAKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIM 466
               +     +Q V +A+ L  +A +LI DEPT  +D G   E+ R+I +L  +G A++ 
Sbjct: 146 APLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDEGEVRELFRVIAQLRERGMAILF 205

Query: 467 ISSELPEILNLSDRIVVMWEG 487
           ++  L ++  +SDRI V+ +G
Sbjct: 206 VTHFLDQVYAVSDRITVLRDG 226


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: 619
Number of extensions: 31
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: 505
Length adjustment: 35
Effective length of query: 485
Effective length of database: 470
Effective search space:   227950
Effective search space used:   227950
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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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