GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatP in Brucella inopinata BO1

Align ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized)
to candidate WP_008508827.1 BIBO1_RS14870 amino acid ABC transporter ATP-binding protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_774
         (244 letters)



>NCBI__GCF_000182725.1:WP_008508827.1
          Length = 258

 Score =  225 bits (573), Expect = 8e-64
 Identities = 111/222 (50%), Positives = 153/222 (68%), Gaps = 8/222 (3%)

Query: 2   ISIKNVNKWYGDFQVLTDCSTEVKKGEVIVVCGPSGSGKSTLIKCVNALEPFQKGDVIVD 61
           + I+ VNK+YG F  L +    +  G+V  + GPSGSGKSTL++C+N LE +  G++++D
Sbjct: 7   VEIRKVNKYYGPFHALRNVDLSIIPGKVTCLIGPSGSGKSTLLRCINFLEEYDSGEIVID 66

Query: 62  GTSIAD--------PKTNLPKLRSRVGMVFQHFELFPHLSIMDNLTIAQVKVLGRSKEEA 113
           G  I          P   L ++R  +GMVFQ F L+PH++ + N+    ++V G  K EA
Sbjct: 67  GQLIGYVSPGGRKMPGRKLREMRRSIGMVFQQFNLWPHMTALQNVAEGLIRVRGLPKSEA 126

Query: 114 SKKALQLLERVGLSAHAKKHPGQLSGGQQQRVAIARALAMDPIVMLFDEPTSALDPEMVN 173
             +A + L++VGL+     HP +LSGGQQQRVAIARA+AM+P +MLFDEPTSALDPE+V 
Sbjct: 127 EARAAEALKKVGLADKMANHPSRLSGGQQQRVAIARAIAMEPRLMLFDEPTSALDPELVG 186

Query: 174 EVLDVMVQLAHEGMTMMCVTHEMGFARKVADRVIFMDQGKII 215
           EVL VM  LA EGMTM+ VTHEMGFA  VAD+V FM++G+++
Sbjct: 187 EVLSVMKTLASEGMTMVVVTHEMGFAAHVADQVAFMEKGELV 228


Lambda     K      H
   0.321    0.135    0.390 

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: 218
Number of extensions: 6
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: 258
Length adjustment: 24
Effective length of query: 220
Effective length of database: 234
Effective search space:    51480
Effective search space used:    51480
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 24 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