GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ytfR in Azospirillum brasilense Sp245

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate AZOBR_RS31210 AZOBR_RS31210 sugar ABC transporter ATP-binding protein

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



>FitnessBrowser__azobra:AZOBR_RS31210
          Length = 516

 Score =  624 bits (1610), Expect = 0.0
 Identities = 321/496 (64%), Positives = 389/496 (78%), Gaps = 4/496 (0%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           +L   GLSK F GV+ALD VDF++R GEI ALLGENGAGKSTLIK LTGVY  D GT+ L
Sbjct: 12  LLAIRGLSKAFLGVQALDGVDFTVRHGEIHALLGENGAGKSTLIKTLTGVYQRDAGTVTL 71

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128
           EG+AI+P+    AQ+L IGTVYQEVNLLPN+SVA+NLF+GR+P RFGL+ R  M +RA  
Sbjct: 72  EGRAIAPRGVEEAQRLHIGTVYQEVNLLPNLSVAENLFLGRQPMRFGLVDRGAMRRRARA 131

Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188
           ++  YG +LDV  PL RFSVA QQIVAI RA+D+SAKVLILDEPTASLD QEV +LF +M
Sbjct: 132 VLIPYGLTLDVTAPLGRFSVATQQIVAIARAVDMSAKVLILDEPTASLDAQEVAVLFKVM 191

Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELDT 248
           R LR RG+ ++FVTHFLDQVY + DRITVLRNG  VG R T ELP+++LV MMLGREL+ 
Sbjct: 192 RTLRSRGIGIVFVTHFLDQVYALCDRITVLRNGRLVGERRTAELPRLDLVAMMLGRELEA 251

Query: 249 HALQRAGRTLLSDK----PVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAE 304
            A + A     +++    P+  F+ YGK  ++ PFDL++RPGE+VGLAGLLGSGRTETA 
Sbjct: 252 VAHRIAPPADDAEEDARPPLVRFRGYGKARSVEPFDLDIRPGEVVGLAGLLGSGRTETAR 311

Query: 305 VIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQ 364
           ++FG+  AD G A + G+   LR P  A  LG GFCPEDRK +GI+ A SVRENIILALQ
Sbjct: 312 LVFGMDRADRGEAAVDGQAVRLRGPRDAIRLGFGFCPEDRKKEGIVGALSVRENIILALQ 371

Query: 365 AQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFL 424
           A++GWLRPI R  Q+EIA+RFIR L IRTP  EQPI+ LSGGNQQK LL+RWL T P+ L
Sbjct: 372 ARQGWLRPIPRCRQEEIADRFIRLLDIRTPHAEQPIQLLSGGNQQKALLARWLATEPRLL 431

Query: 425 ILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEI 484
           ILDEPTRGIDVGAHAEIIRLIE LCADG+ALLV+SSELEE+V Y+ RV+++RDR+ VAE+
Sbjct: 432 ILDEPTRGIDVGAHAEIIRLIERLCADGMALLVVSSELEEIVAYSRRVVVLRDRRHVAEL 491

Query: 485 PLAELSVPAIMNAIAA 500
              E++V  I+ AIA+
Sbjct: 492 RGGEVAVDRIVAAIAS 507


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: 756
Number of extensions: 30
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 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