GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfR in Bradyrhizobium sp. BTAi1

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate WP_012042345.1 BBTA_RS09915 sugar ABC transporter ATP-binding protein

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



>NCBI__GCF_000015165.1:WP_012042345.1
          Length = 516

 Score =  576 bits (1484), Expect = e-169
 Identities = 292/493 (59%), Positives = 376/493 (76%), Gaps = 1/493 (0%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           +L   GL+K F  +KAL +VDF+L  GEI ALLGENGAGKSTLIK +TGV+  D GT+ L
Sbjct: 14  LLEIRGLTKSFGALKALQDVDFTLGEGEIHALLGENGAGKSTLIKVVTGVFARDAGTVRL 73

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128
            G  I+P++   A + GI TVYQEVNLLPN+SVA NL++GR+P RFG++R+ EM +RA  
Sbjct: 74  AGDEIAPRSAKDAVEAGIATVYQEVNLLPNLSVAQNLYLGRQPTRFGVVRQAEMRRRAHA 133

Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188
           L+  YG  +DV  PL  +SVA+Q I AI RA+DLSA+VLILDEPTASLD  EVE+LF +M
Sbjct: 134 LLLDYGLDIDVGAPLASYSVAVQHITAIARAVDLSARVLILDEPTASLDRHEVEILFRVM 193

Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELDT 248
           R+L   G+ ++FV+HFLDQVY++ DR+TVLRNG  +G R+  +LP+++L++MMLGREL  
Sbjct: 194 RKLAADGIGIVFVSHFLDQVYEICDRVTVLRNGRLIGTRDITDLPRLDLIRMMLGRELAE 253

Query: 249 HALQRAGRTLLSDKPVA-AFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIF 307
              +RA     + + V  +FK +GK+G +APFDLE+R GE+VGLAGLLGSGRTETA ++F
Sbjct: 254 TTHERAASQPDTAREVCVSFKGFGKQGYVAPFDLELRRGEVVGLAGLLGSGRTETARLVF 313

Query: 308 GIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQR 367
           G + ADSG A + GK   L SP  A+ LG G+CPE+RKT+GI+A  +VRENI+LALQA+R
Sbjct: 314 GAERADSGEASVAGKAVRLNSPRDAAGLGFGYCPEERKTEGIVADLTVRENIVLALQARR 373

Query: 368 GWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILD 427
           G  RP+SR+EQ EIA R+IR L IR P  E+PI  LSGGNQQK LL+RWL T P+ L+LD
Sbjct: 374 GLHRPLSRREQDEIAMRYIRMLDIRPPDPERPIGLLSGGNQQKALLARWLATSPKLLVLD 433

Query: 428 EPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLA 487
           EPTRGIDVGAHAEIIRL+  LC  GLALLVISSEL+E+V Y++RV+++RDR  V E+   
Sbjct: 434 EPTRGIDVGAHAEIIRLVRDLCEQGLALLVISSELDEIVTYSNRVVVLRDRAHVEELKGD 493

Query: 488 ELSVPAIMNAIAA 500
            + V +I+ AIAA
Sbjct: 494 AVEVSSILAAIAA 506


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: 678
Number of extensions: 29
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: 516
Length adjustment: 34
Effective length of query: 466
Effective length of database: 482
Effective search space:   224612
Effective search space used:   224612
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 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