Alignments for a candidate for xylK_Tm in Moritella dasanensis ArB 0140

GapMind for catabolism of small carbon sources

Alignments for a candidate for xylK_Tm in Moritella dasanensis ArB 0140

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_017221119.1 A923_RS0107850 ribose ABC transporter ATP-binding protein RbsA

Query= uniprot:Q9WXX0
         (520 letters)



>NCBI__GCF_000276805.1:WP_017221119.1
          Length = 501

 Score =  404 bits (1037), Expect = e-117
 Identities = 221/500 (44%), Positives = 318/500 (63%), Gaps = 9/500 (1%)

Query: 14  ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73
           ILK  GI K FPGV A+DN    VY  ++++L+GENGAGKSTL+K+LTG+   D G I  
Sbjct: 5   ILKLSGIEKSFPGVKALDNACLNVYPGKVMALLGENGAGKSTLMKVLTGIYHMDKGSINY 64

Query: 74  NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133
            G  V F  P  + + GIS+IHQELNL   +T+AENI+L  E            +    M
Sbjct: 65  QGSDVTFDGPRHSQEVGISIIHQELNLIPELTIAENIYLGRETTNA-----FGGIKWTQM 119

Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193
           +  +  LL  +  K S   L+  L+  ++QMVEI KAL  + ++I MDEPT +LT  ET+
Sbjct: 120 FADADALLQRLNVKHSSRQLLGELSLGEQQMVEIAKALSFKSQVIVMDEPTDALTESETK 179

Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253
            LF++I  L++ G  +V++SHRL E+  I D I V+RDGK I E+   + D D +I+ MV
Sbjct: 180 SLFKVINELRNEGCGIVYISHRLKEIFEICDDITVLRDGKFIAEIAVTDIDEDGLIEKMV 239

Query: 254 GREVEFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETMLL 313
           GR ++     I+ + G + LEV N+     V++VSF +  GE+LG +GL+GAGRTE M  
Sbjct: 240 GRRLDEIYPRIDAKHGTLCLEVENIV-APGVRDVSFTLDHGEILGISGLMGAGRTELMKA 298

Query: 314 VFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSLK 373
           ++G   ++SGD+ ++ + V    P D +  GI  I EDRK  GL+L ++VK+N+ L +L 
Sbjct: 299 IYGALPRQSGDVILDDKVVSPITPRDGLANGIAYISEDRKGDGLILGLSVKENMSLCALD 358

Query: 374 KISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADIL 433
            +S+ GL LD  KE    ED++++ ++KTPS  QI  NLSGGNQQKV +AK L T   +L
Sbjct: 359 ALSK-GLQLDHAKEATAVEDFMRQFNVKTPSRDQIIGNLSGGNQQKVAIAKGLMTRPKVL 417

Query: 434 IFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAVL 493
           I DEPTRG+DVGAK EI+++I +  A+G ++I++SSE+PE+L +SDRI+VM EG I+   
Sbjct: 418 ILDEPTRGVDVGAKKEIYQLINQFKAEGMSIILVSSEMPEVLGMSDRILVMHEGRISG-- 475

Query: 494 DNREKRVTQEEIMYYASGQK 513
           +       QE++M  A G+K
Sbjct: 476 EFMAADANQEKLMACAVGKK 495



 Score =  104 bits (260), Expect = 7e-27
 Identities = 64/232 (27%), Positives = 126/232 (54%), Gaps = 8/232 (3%)

Query: 30  VDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILVNGERVEFHSPVDAFKK 89
           V +V F +   EI+ + G  GAG++ L+K + G L   +G+++++ + V   +P D    
Sbjct: 269 VRDVSFTLDHGEILGISGLMGAGRTELMKAIYGALPRQSGDVILDDKVVSPITPRDGLAN 328

Query: 90  GISVIHQELN---LCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYMYTRSKELLDLIGA 146
           GI+ I ++     L   ++V EN+ L   A+    + L  ++D     T  ++ +     
Sbjct: 329 GIAYISEDRKGDGLILGLSVKENMSLC--ALDALSKGL--QLDHAKEATAVEDFMRQFNV 384

Query: 147 KF-SPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETERLFEIIEMLKSR 205
           K  S D ++ NL+   +Q V I K L+  P+++ +DEPT  + V   + ++++I   K+ 
Sbjct: 385 KTPSRDQIIGNLSGGNQQKVAIAKGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKAE 444

Query: 206 GISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMVGREV 257
           G+S++ VS  + EV+ +SDRI+VM +G+  GE    + + + ++   VG+++
Sbjct: 445 GMSIILVSSEMPEVLGMSDRILVMHEGRISGEFMAADANQEKLMACAVGKKI 496


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: 709
Number of extensions: 39
Number of successful extensions: 8
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: 520
Length of database: 501
Length adjustment: 34
Effective length of query: 486
Effective length of database: 467
Effective search space:   226962
Effective search space used:   226962
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 24 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:

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 2024 update 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