GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Sinorhizobium meliloti 1021

Align Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized)
to candidate SMa0083 SMa0083 ABC transporter ATP-binding protein

Query= TCDB::P0AAG3
         (241 letters)



>FitnessBrowser__Smeli:SMa0083
          Length = 259

 Score =  274 bits (700), Expect = 1e-78
 Identities = 138/240 (57%), Positives = 175/240 (72%), Gaps = 4/240 (1%)

Query: 2   ITLKNVSKWYGHFQVLTDCSTEVKKGEVVVVCGPSGSGKSTLIKTVNGLEPVQQGEITVD 61
           + ++ V+KWY  F  L +    V +GE +V+CGPSGSGKSTLI+ +N LE +  G I VD
Sbjct: 21  VRMEGVNKWYDAFHALKNIDLTVGRGERIVICGPSGSGKSTLIRCINQLETIHSGRIVVD 80

Query: 62  G--IVVNDKKTDLAKLRSRVGMVFQHFELFPHLSIIENLTLAQVKVLKRDKAPAREKALK 119
           G  +    +  DL  +R   GMVFQ F LFPH++++EN TLA +KV    KA A E A+K
Sbjct: 81  GHDLTAGGRNVDL--VRQETGMVFQQFNLFPHMTVLENCTLAPMKVRGLAKAEAEETAMK 138

Query: 120 LLERVGLSAHANKFPAQLSGGQQQRVAIARALCMDPIAMLFDEPTSALDPEMINEVLDVM 179
            L+RV +   A K+PAQLSGGQQQRVAIARALCM+P  MLFDEPTSALDPEM+ EVLD M
Sbjct: 139 YLKRVRIPEQAVKYPAQLSGGQQQRVAIARALCMNPKIMLFDEPTSALDPEMVKEVLDTM 198

Query: 180 VELANEGMTMMVVTHEMGFARKVANRVIFMDEGKIVEDSPKDAFFDDPKSDRAKDFLAKI 239
           V+LANEGMTM+ VTHEMGFAR VA+RV+FMD G+++E +P DAFF  P+ +R + FL +I
Sbjct: 199 VDLANEGMTMLCVTHEMGFARSVADRVVFMDRGEVLEIAPPDAFFGAPQHERTRFFLGQI 258


Lambda     K      H
   0.320    0.135    0.383 

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: 188
Number of extensions: 8
Number of successful extensions: 1
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: 241
Length of database: 259
Length adjustment: 24
Effective length of query: 217
Effective length of database: 235
Effective search space:    50995
Effective search space used:    50995
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: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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