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_b21344 SM_b21344 sugar uptake ABC transporter ATP-binding protein

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



>FitnessBrowser__Smeli:SM_b21344
          Length = 497

 Score =  422 bits (1085), Expect = e-122
 Identities = 225/492 (45%), Positives = 314/492 (63%), Gaps = 1/492 (0%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           +L  +G+ K F G+ AL      +   E+MAL+G+NGAGKSTLIK LTG Y  D G +  
Sbjct: 2   LLSMQGICKSFNGIPALRAASLEVGEAEVMALVGQNGAGKSTLIKILTGAYRRDEGAVVF 61

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128
            G+ +S    A +Q  GI T+YQE+NL P  SVA+N+++ REP+RFGL+ R+ M   A  
Sbjct: 62  AGEGVSFSMPAESQARGIATIYQEINLAPQRSVAENIYLSREPRRFGLIDRRAMRDGAAA 121

Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188
           ++ ++   +DV +P+  FS A +Q+VAI RA+   A+++I+DEPT+SLD +EV +LFD +
Sbjct: 122 VLRAFNLEIDVDQPVAGFSAATRQMVAIARAVTQKARLVIMDEPTSSLDEREVGILFDTI 181

Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELDT 248
           R L+  GVS++F+ H L+++Y++ DR+T++R+G  V      ++P++ LV+ MLG+EL  
Sbjct: 182 RTLKRGGVSVVFIGHRLEELYRICDRVTIMRDGKTVATAAMADMPKLALVRHMLGKELAA 241

Query: 249 HALQRAGRTLLSDKPV-AAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIF 307
                      + +PV  + +N G    +    L VR GEI GLAGLLGSGRTETA +IF
Sbjct: 242 FEAIAKDADEGAQRPVRLSVRNAGAGVRVRDVSLTVREGEISGLAGLLGSGRTETANLIF 301

Query: 308 GIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQR 367
           G      G     G+ +  R P  A   GIG   EDRK DGII   S+REN+ LAL  + 
Sbjct: 302 GADRLQRGEIRYNGEARAYRQPADAIADGIGLVAEDRKVDGIIPDMSIRENMTLALLPKL 361

Query: 368 GWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILD 427
                + R  Q EI ER+I  L I+  S +QPI+ LSGGNQQKVLL RWL T P+ LI+D
Sbjct: 362 ARAGIVDRARQDEIVERYITALAIKCTSPDQPIKELSGGNQQKVLLGRWLCTDPKLLIVD 421

Query: 428 EPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLA 487
           EPTRGID+GA +EI+RL+  L  +GL +L+ISSELEEL+  ADRV ++ D   VA +P  
Sbjct: 422 EPTRGIDIGAKSEILRLLRRLADEGLGVLMISSELEELLAAADRVTVLSDGTSVAVLPRK 481

Query: 488 ELSVPAIMNAIA 499
           ELS  A+  A+A
Sbjct: 482 ELSEAALFAAMA 493


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: 614
Number of extensions: 28
Number of successful extensions: 6
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: 497
Length adjustment: 34
Effective length of query: 466
Effective length of database: 463
Effective search space:   215758
Effective search space used:   215758
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