GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braD in Azospirillum brasilense Sp245

Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate AZOBR_RS03565 AZOBR_RS03565 branched-chain amino acid ABC transporter permease

Query= uniprot:Q1MCU0
         (300 letters)



>FitnessBrowser__azobra:AZOBR_RS03565
          Length = 304

 Score =  234 bits (598), Expect = 1e-66
 Identities = 122/297 (41%), Positives = 186/297 (62%), Gaps = 8/297 (2%)

Query: 3   YFVQQLLNGLTLGSIYGLVAIGYTMVYGIIGMINFAHGDIFMLGGFAALIVFLVLTSIFA 62
           +F+QQL+N  T+  +YGL+A+GYT+VYGI+G IN A G++ M+G     +    L     
Sbjct: 3   FFLQQLINAATVACVYGLLALGYTLVYGILGQINLAMGELTMIGAMLTAMGAAALGMAGL 62

Query: 63  G-LPVAVLLLVMLVVAMLMTSLWNWTIERVAYRPLRGSFRLAPLITAIGMSITLSNFIQV 121
           G LP+AVL +   V+A   T++  WT++R+ +R LR +    PLI A+G+SI     +++
Sbjct: 63  GSLPLAVLGVFATVMAF--TAVQGWTMDRLVFRRLRRTHNHTPLIAAVGLSIAYQEGMRL 120

Query: 122 TQGPRNKPIPPMVSSVYQFGN-----ISVSLKQIIIIVITAVLLTIFWYIVNRTALGRAQ 176
             G R+      ++  ++  +     ++    Q +I+++T  L  + W I+ RTA GRA 
Sbjct: 121 LHGARDWWPAQFLADRHELLSDGAFTVTALTSQAVILLMTGGLYALLWAIMQRTAYGRAH 180

Query: 177 RATEQDRKMAALLGVNVDQTISITFVMGAALAAVAGTMYLMYYGVASFNDGFTPGVKAFT 236
           RA   D   A L+GV+VD+T++ TF +G ALAA AG +  +YYG  +F  G+  G KA  
Sbjct: 181 RACADDVGAAELVGVDVDRTVATTFAVGGALAAAAGAVIALYYGGVNFYTGYLVGFKALA 240

Query: 237 AAVLGGIGSLPGAVFGGLLIGLIESLWSAYFTIAYKDVATFAILAFVLIFKPTGILG 293
           AAV+GGIGS+PGA+ GG L+GL+E+ WSAYF IAYKD+  F +L   LI++P G++G
Sbjct: 241 AAVVGGIGSVPGAMLGGALLGLVETFWSAYFAIAYKDIVAFGLLTLFLIYRPDGLMG 297


Lambda     K      H
   0.329    0.143    0.421 

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: 343
Number of extensions: 17
Number of successful extensions: 4
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: 300
Length of database: 304
Length adjustment: 27
Effective length of query: 273
Effective length of database: 277
Effective search space:    75621
Effective search space used:    75621
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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