GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfR in Sinorhizobium meliloti 1021

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate SM_b21376 SM_b21376 sugar uptake ABC transporter ATP-binding protein

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



>FitnessBrowser__Smeli:SM_b21376
          Length = 503

 Score =  367 bits (941), Expect = e-106
 Identities = 200/488 (40%), Positives = 299/488 (61%), Gaps = 2/488 (0%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           IL+   ++K F  V AL  +   +RRG +  LLGENGAGKSTL+K L GV+ A  G I L
Sbjct: 9   ILKITDVTKSFGQVAALKGMRLEVRRGRVHTLLGENGAGKSTLMKILAGVHGATSGEIVL 68

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128
           +GQA  P N   A  LG+  V+QE++L  N++VA+N+   REP+RFG +  K +  +A  
Sbjct: 69  DGQAYRPANPQEAASLGLAIVFQELSLCNNLTVAENILATREPRRFGFINDKALVAKAHR 128

Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188
           ++A     +DV E +   S+A +Q+V I + +   AKV+ILDEPT+SL   E E+LF+++
Sbjct: 129 IVADLRLPIDVTEKVGNLSIAQRQLVEIAKGLSHDAKVVILDEPTSSLSDSEAEILFEII 188

Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELDT 248
            +LR RG ++I+++H ++++ ++SD ITV+R+G +V      E+    L+ +M+GR +D 
Sbjct: 189 GRLRQRGAAIIYISHRMEEIMRLSDDITVIRDGEYVSTHARDEVTIETLIALMVGRRMDE 248

Query: 249 HALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFG 308
                         PV A     ++G       +VR GEI+G  GL+GSGR+E    +FG
Sbjct: 249 IYPPPVHHVAADRAPVLAVDRLTREGEFQDVSFDVRAGEILGFFGLVGSGRSEVMNALFG 308

Query: 309 IKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQ-R 367
           +K A +GT  + G+    RSP QA   G+GF  E+RK +G++   SV  NI +A  A   
Sbjct: 309 MKSA-AGTVRLDGEVVRFRSPDQAIARGVGFVTENRKEEGLVLGHSVEWNISMAALADFA 367

Query: 368 GWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILD 427
           G L  I    ++  A   + +L I+T S E P   LSGGNQQK++L++WLLTRP+ LILD
Sbjct: 368 GGLGFIRNGAERAAASEQVGKLSIKTNSLETPAGALSGGNQQKIVLAKWLLTRPKVLILD 427

Query: 428 EPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLA 487
           EPTRG+DVGA  EI ++I  L A+G A+L+ISS+L E++G +DRV++M +    A +  +
Sbjct: 428 EPTRGVDVGAKFEIYKIIRELAAEGTAILLISSDLPEVLGMSDRVVVMHEGAPGATLEGS 487

Query: 488 ELSVPAIM 495
            L+   IM
Sbjct: 488 ALTPETIM 495


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: 623
Number of extensions: 39
Number of successful extensions: 8
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: 500
Length of database: 503
Length adjustment: 34
Effective length of query: 466
Effective length of database: 469
Effective search space:   218554
Effective search space used:   218554
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.

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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