GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpP in Azospirillum brasilense Sp245

Align GlpP, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate AZOBR_RS25885 AZOBR_RS25885 ABC transporter permease

Query= TCDB::G3LHZ0
         (288 letters)



>FitnessBrowser__azobra:AZOBR_RS25885
          Length = 294

 Score =  428 bits (1100), Expect = e-125
 Identities = 208/290 (71%), Positives = 241/290 (83%), Gaps = 5/290 (1%)

Query: 1   MQKTWNNKAWFLVLPVLLLVAFSAVIPLMTVVNYSVQDTFGNNEFFWAGTDWFVQTLHSD 60
           M K  N  AW LVLPVLL+VAFSA++PLMTVVNYSVQDTFGNN+FFW G  W+ + L   
Sbjct: 1   MDKPVNQGAWLLVLPVLLIVAFSAILPLMTVVNYSVQDTFGNNQFFWNGIGWYQELLDPS 60

Query: 61  -----RFWESLQRNLLFSFIILALEIPLGIFIALNMPKSGPGVPVCLVLMALPLLIPWNV 115
                RF+++L RNLLFS +IL +E+PLGI +AL+MP+ G  V   LV++ALPLLIPWNV
Sbjct: 61  TDLGGRFFDALWRNLLFSLLILLIEVPLGIAVALSMPRHGWRVAATLVVLALPLLIPWNV 120

Query: 116 VGTIWQVFGRVDIGLLGHTLEAIGLDYNYVRDPIDAWVTVIVMDVWHWTSLVVLLCYAGL 175
           VGTIWQ+F R DIGLLG  +  +G+ YNY  DP+ AWVT++VMDVWHWTSLV LLCYAGL
Sbjct: 121 VGTIWQIFAREDIGLLGWAVNRLGIPYNYTADPLSAWVTIVVMDVWHWTSLVALLCYAGL 180

Query: 176 VSIPDAYYQAAKIDGASRWSVFRYIQLPKMKRVLLIAVLLRFMDSFMIYTEPFVVTGGGP 235
            SIPDA+YQAA+IDGASRW+VFR IQLPKM RVLLIAVLLRFMDSFMIYTEPFVVTGGGP
Sbjct: 181 RSIPDAFYQAARIDGASRWAVFRNIQLPKMHRVLLIAVLLRFMDSFMIYTEPFVVTGGGP 240

Query: 236 GNSTTFLSIDLVKMAVGQFDLGPAAAMSIIYFLIILLLSWVFYTVMTSSD 285
           GNSTTF+SIDLVK+A+GQFDLG AAA+SI+Y LIIL + WVFYTVMT  D
Sbjct: 241 GNSTTFVSIDLVKLALGQFDLGKAAALSIVYNLIILAVCWVFYTVMTRMD 290


Lambda     K      H
   0.329    0.143    0.464 

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: 392
Number of extensions: 14
Number of successful extensions: 2
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: 288
Length of database: 294
Length adjustment: 26
Effective length of query: 262
Effective length of database: 268
Effective search space:    70216
Effective search space used:    70216
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