GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfR in Klebsiella michiganensis M5al

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>FitnessBrowser__Koxy:BWI76_RS07240
          Length = 494

 Score =  389 bits (1000), Expect = e-112
 Identities = 199/469 (42%), Positives = 308/469 (65%), Gaps = 4/469 (0%)

Query: 10  LRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLE 69
           L  EG+SKFFPGVKALDNV   +R G + AL+GENGAGKSTL+K L G+Y  D+G I ++
Sbjct: 6   LEAEGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIRVK 65

Query: 70  GQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATEL 129
           G+ +  ++T  A + GI  ++QE+NL+P+M+VA+N+++GREP ++G +  +++ ++  +L
Sbjct: 66  GEPVQFQDTMDALRSGISMIHQELNLVPHMTVAENIWLGREPMKYGFVDHRQLARQTQDL 125

Query: 130 MASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMR 189
           +      L     +   S+A QQ+V I +A+  +A ++I+DEPT++L   EV  LF ++R
Sbjct: 126 LDKLNIRLSADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTIIR 185

Query: 190 QLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELDTH 249
            LR +G ++I+++H +D+++ ++D I+V R+G++VG ++T E  +  L+  M+GREL T 
Sbjct: 186 DLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQMVGREL-TQ 244

Query: 250 ALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGI 309
              +    +   + V   +N  +KG     +  VR GEI+G+AGL+G+GR+E  E +FG+
Sbjct: 245 LFPKFNNAI--GEEVLTVRNLSRKGAFHDINFSVRRGEILGVAGLVGAGRSEVMESLFGM 302

Query: 310 KPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENI-ILALQAQRG 368
           + ADSG  LI G P N+ SP  A   G+    EDRK  G+    SV EN+ I+ +    G
Sbjct: 303 EKADSGEVLIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENMSIVKMPEYIG 362

Query: 369 WLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDE 428
               +   +  E     IR+L I+TP+ +Q I  LSGGNQQKVL++RWLL +P+ LILDE
Sbjct: 363 KTGFVQHLKMAEDCMEQIRRLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQPKILILDE 422

Query: 429 PTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRD 477
           PTRGIDVGA AEI  LI  L   G+A++++SSEL E++G +DRV++M +
Sbjct: 423 PTRGIDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHE 471



 Score = 99.0 bits (245), Expect = 3e-25
 Identities = 67/227 (29%), Positives = 121/227 (53%), Gaps = 13/227 (5%)

Query: 7   QEILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTI 66
           +E+L    LS+      A  +++FS+RRGEI+ + G  GAG+S ++++L G+  AD G +
Sbjct: 255 EEVLTVRNLSR----KGAFHDINFSVRRGEILGVAGLVGAGRSEVMESLFGMEKADSGEV 310

Query: 67  WLEGQAISPKNTAHAQQLGIGTVYQE---VNLLPNMSVADNLFIGREPKRFGLLRRKEME 123
            ++G  ++  + + A + G+  + ++     L   +SV +N+ I + P+  G     +  
Sbjct: 311 LIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENMSIVKMPEYIGKTGFVQHL 370

Query: 124 KRATELMASYGFSLDVREP-----LNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDT 178
           K A + M      L+++ P     +N  S   QQ V I R +    K+LILDEPT  +D 
Sbjct: 371 KMAEDCMEQIR-RLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQPKILILDEPTRGIDV 429

Query: 179 QEVELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVG 225
                ++ L+ +L +RGV++I V+  L ++  +SDR+ V+  G   G
Sbjct: 430 GAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHEGRITG 476


Lambda     K      H
   0.321    0.138    0.391 

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: 600
Number of extensions: 30
Number of successful extensions: 7
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: 500
Length of database: 494
Length adjustment: 34
Effective length of query: 466
Effective length of database: 460
Effective search space:   214360
Effective search space used:   214360
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 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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