GapMind for catabolism of small carbon sources

 

Aligments for a candidate for xylK_Tm in Pseudomonas fluorescens FW300-N1B4

Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate Pf1N1B4_6034 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= uniprot:Q9WXX0
         (520 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_6034 Ribose ABC transport
           system, ATP-binding protein RbsA (TC 3.A.1.2.1)
          Length = 517

 Score =  329 bits (843), Expect = 2e-94
 Identities = 191/508 (37%), Positives = 306/508 (60%), Gaps = 16/508 (3%)

Query: 14  ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73
           +L   GI K +   V +  +D  +   E+++L GENGAGKSTL KI+ G++ P  G++  
Sbjct: 9   VLSVSGIGKTYAQPV-LTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVAPTTGQMRF 67

Query: 74  NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133
            G      S   A + GI ++ QELNL   ++VAEN+FL      G        +    +
Sbjct: 68  QGRDYRPGSRSQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSHG------GWISRKQL 121

Query: 134 YTRSKELLDLIGAK-FSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEET 192
              + E +  +G     PD LV  L    +QMVEI + L+ +  ++ +DEPT+ LT  E 
Sbjct: 122 RKAAIEAMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREV 181

Query: 193 ERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMM 252
           E LFE I  L++RG+S++++SHRL+E+ R++ RI V+RDG  +       ++ + ++ +M
Sbjct: 182 EMLFEQITRLQARGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLM 241

Query: 253 VGREVEFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETML 312
           VGRE+         + G  AL V+ L   DKV++VSFEVR GE+ G +GL+GAGRTE + 
Sbjct: 242 VGRELGEHIDMGPRKIGAPALTVKGLTRSDKVRDVSFEVRAGEIFGISGLIGAGRTELLR 301

Query: 313 LVFGVNQKESGDIYV--NGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLP 370
           L+FG +  +SG + +  + + V I++P DA+  GI LI EDRK +GL+L  ++  NI L 
Sbjct: 302 LIFGADTADSGTVALGASAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANIALG 361

Query: 371 SLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNA 430
           ++  IS  G V +   E  +++  +  + I++ S  Q+   LSGGNQQKVV+ +WL  + 
Sbjct: 362 NMPVISSGGFV-NNGDEMSLAQRQINAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDC 420

Query: 431 DILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEIT 490
            +++FDEPTRGIDVGAK +I+ ++ EL  QGKA++++SS+L E++ + DRI V+  G + 
Sbjct: 421 TVMLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRL- 479

Query: 491 AVLDNREK-RVTQEEIMYYA-SGQKKQN 516
             +D  E+   TQ++++  A +G +K++
Sbjct: 480 --IDTFERDSWTQDDLLAAAFAGYQKRD 505


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: 631
Number of extensions: 42
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 520
Length of database: 517
Length adjustment: 35
Effective length of query: 485
Effective length of database: 482
Effective search space:   233770
Effective search space used:   233770
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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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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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