GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natA in Magnetospirillum magneticum AMB-1

Align NatA, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized)
to candidate WP_011384082.1 AMB_RS08465 ABC transporter ATP-binding protein

Query= TCDB::Q7A2H0
         (260 letters)



>NCBI__GCF_000009985.1:WP_011384082.1
          Length = 253

 Score =  182 bits (463), Expect = 5e-51
 Identities = 97/254 (38%), Positives = 149/254 (58%), Gaps = 7/254 (2%)

Query: 9   LPLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRV 68
           + LL    L K FGG+ AV++    V  G I  +IGPNGAGKTTLFNL++    P  GRV
Sbjct: 1   MSLLKVEKLSKEFGGVHAVEDLTFSVEAGHIHSIIGPNGAGKTTLFNLITGVYTPSSGRV 60

Query: 69  IFDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQV 128
           +F    +  ++P+++A+ GM RTFQ  +    +  +EN+++         F    L+   
Sbjct: 61  LFQDRLVSGMKPYELAELGMSRTFQNLQIFFNMQAIENVMVGHHLHLDRRFLPSLLRLPK 120

Query: 129 VVKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAA 188
           V + +++ +E    L+E VGL K     A  +  G  K LE+ RAL   PKL+LLDEPAA
Sbjct: 121 VTRRDRECREYCAGLMEFVGLGKYLDADAASMPYGALKRLEIARALAAQPKLLLLDEPAA 180

Query: 189 GVN---PRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPA 245
           G+N    R ID++  ++ T     G+T +++EH+M ++M + D++  L  G+ LA+GTPA
Sbjct: 181 GLNATESREIDEVIKKVAT----TGVTVVLVEHDMKMVMGISDQITALDYGRKLAEGTPA 236

Query: 246 EIQTNSQVLEAYLG 259
           E++ N +V+ AYLG
Sbjct: 237 EVRANPEVVSAYLG 250


Lambda     K      H
   0.319    0.136    0.391 

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: 138
Number of extensions: 4
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: 260
Length of database: 253
Length adjustment: 24
Effective length of query: 236
Effective length of database: 229
Effective search space:    54044
Effective search space used:    54044
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 (21.7 bits)
S2: 47 (22.7 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