GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Sinorhizobium meliloti 1021

Align ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized)
to candidate SMa0489 SMa0489 ABC transporter ATP-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4773
         (244 letters)



>FitnessBrowser__Smeli:SMa0489
          Length = 255

 Score =  275 bits (702), Expect = 8e-79
 Identities = 141/244 (57%), Positives = 177/244 (72%), Gaps = 2/244 (0%)

Query: 1   MISIKSINKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDIVV 60
           MI +  + K +G F+ L   S EV++GE IV+CGPSGSGKSTLI+C+N +E    G I++
Sbjct: 14  MIQLIGVGKRFGQFEALKQVSLEVRRGEKIVLCGPSGSGKSTLIRCINRMEEHTSGRIII 73

Query: 61  DGTSIADPKTNLPKLRSRVGMVFQHFELFPHLTITENLTIAQIKVLGRSKEEATKKGLQL 120
           DG  + D   ++  +R  VGMVFQ F LFPH+TI +NLTIAQ  V    ++EA +  +  
Sbjct: 74  DGRELTDRTKDINAVRREVGMVFQSFNLFPHMTILKNLTIAQRLVRKTPEKEAKEVAMHY 133

Query: 121 LERVGLSAHAHKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVNEVLDVMV 180
           L+RV +   A K+P QLSGGQQQRVAIARAL M P +MLFDEPTSALDPEM++EVLDVMV
Sbjct: 134 LKRVKIPEQASKYPVQLSGGQQQRVAIARALCMKPQIMLFDEPTSALDPEMISEVLDVMV 193

Query: 181 QLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKIIEDCKKEEFFGDINARAERTQHFLNK 240
            LA +GMTM+CVTHEMGFAR VADRV+FMD G++IE+   E FF   N R ERT  FL +
Sbjct: 194 DLARDGMTMICVTHEMGFARSVADRVMFMDGGQLIEEGDPETFFA--NPRNERTALFLRQ 251

Query: 241 ILQH 244
           IL+H
Sbjct: 252 ILRH 255


Lambda     K      H
   0.321    0.136    0.394 

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: 205
Number of extensions: 7
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: 244
Length of database: 255
Length adjustment: 24
Effective length of query: 220
Effective length of database: 231
Effective search space:    50820
Effective search space used:    50820
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 (21.9 bits)
S2: 46 (22.3 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