GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylK_Tm in Tistlia consotensis USBA 355

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_085124759.1 B9O00_RS21320 sugar ABC transporter ATP-binding protein

Query= uniprot:Q9WXX0
         (520 letters)



>NCBI__GCF_900177295.1:WP_085124759.1
          Length = 518

 Score =  343 bits (880), Expect = 9e-99
 Identities = 191/496 (38%), Positives = 293/496 (59%), Gaps = 12/496 (2%)

Query: 14  ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73
           +L+ +G+ +RFPGV+A+D VDF++   E+  L GENGAGKST+I ++ G L+P  GE   
Sbjct: 23  LLELRGVSRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSEGEFRF 82

Query: 74  NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133
            GE VE +S   A   GIS + QE +L   MTV EN+FL  E+ R         +D   +
Sbjct: 83  RGEPVELNSVHHARGLGISAVFQEFSLVPQMTVEENLFLGAESTR------LGLLDRRAL 136

Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193
           + R+  +L  +G    P   V +LT A++QMVEI KA   E  ++ +DEPT+SLT  ET 
Sbjct: 137 HDRADAILKRLGFPLRPRDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASLTERETA 196

Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253
           +LF++IE +K++G+ V++++HRL E+ RI DRI V+RDG+ +  +         ++++M 
Sbjct: 197 QLFKLIEQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELVRLMT 256

Query: 254 GREV-EFFPHGIETRPGEIALEVRNLKW-KDKVKNVSFEVRKGEVLGFAGLVGAGRTETM 311
           GR   E FP  +  +PG   L V  L      V   S  V  GE++G AGLVG+G++E  
Sbjct: 257 GRVYDELFPK-VRFKPGRELLSVERLTTASGSVVEASLSVCAGEIVGLAGLVGSGKSEVA 315

Query: 312 LLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPS 371
              FG+ +   G + + G +V  + P+  +K G   +P DR+ +GL++   V++N+ LPS
Sbjct: 316 RACFGLEKIAEGHVRLKGEEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSLPS 375

Query: 372 LKKISRW-GLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNA 430
           L       G +LD R E +      ++L+++ P I +  E  SGGNQQKV+LAK      
Sbjct: 376 LTLAPFGNGALLDRRGETDRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLAKSRTRPV 435

Query: 431 DILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEIT 490
            +  FDEPT G+DVG +  I+  IR+L   G  +++ISS+LPE+LNLS+R  V + G + 
Sbjct: 436 QVFAFDEPTVGVDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRVQ 495

Query: 491 AVLDNREKRVTQEEIM 506
           A L   E  +T+E+++
Sbjct: 496 AELAGDE--ITEEKVL 509



 Score = 65.5 bits (158), Expect = 5e-15
 Identities = 64/260 (24%), Positives = 106/260 (40%), Gaps = 10/260 (3%)

Query: 1   MFPLLAFRGDRMEILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKIL 60
           +FP + F+  R E+L  + +      VV        V   EIV L G  G+GKS + +  
Sbjct: 263 LFPKVRFKPGR-ELLSVERLTTASGSVV---EASLSVCAGEIVGLAGLVGSGKSEVARAC 318

Query: 61  TGVLKPDAGEILVNGERVEFHSPVDAFKKGISVI---HQELNLCDNMTVAENIFL-AYEA 116
            G+ K   G + + GE V    P    K+G   +    ++  L     V EN+ L +   
Sbjct: 319 FGLEKIAEGHVRLKGEEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSLPSLTL 378

Query: 117 VRGQKRTLSSRVDENYMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPR 176
                  L  R  E     R  E L+L   +   +  V   +   +Q V + K+  +  +
Sbjct: 379 APFGNGALLDRRGETDRVRRLAEQLNLQPPRI--ERAVEAFSGGNQQKVLLAKSRTRPVQ 436

Query: 177 IIFMDEPTSSLTVEETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIG 236
           +   DEPT  + V     ++E I  L   G  ++ +S  L EV+ +S+R  V   G+   
Sbjct: 437 VFAFDEPTVGVDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRVQA 496

Query: 237 ELKKGEFDVDTIIKMMVGRE 256
           EL   E   + ++     R+
Sbjct: 497 ELAGDEITEEKVLSHFFERD 516


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: 674
Number of extensions: 34
Number of successful extensions: 9
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: 518
Length adjustment: 35
Effective length of query: 485
Effective length of database: 483
Effective search space:   234255
Effective search space used:   234255
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 Apr 09 2024. 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