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_043744393.1 AMB_RS12355 ABC transporter ATP-binding protein

Query= TCDB::Q7A2H0
         (260 letters)



>NCBI__GCF_000009985.1:WP_043744393.1
          Length = 243

 Score =  182 bits (462), Expect = 6e-51
 Identities = 99/251 (39%), Positives = 147/251 (58%), Gaps = 15/251 (5%)

Query: 10  PLLAASGLCKSFGGIKAVQEARIEVAQGSITGLIGPNGAGKTTLFNLLSNFIRPDKGRVI 69
           PLL   GL K+F G++AV      VA G +  LIGPNGAGKTT+FN+++    PD+GR+ 
Sbjct: 5   PLLLVEGLVKNFRGLRAVDGVSFSVAAGEVVALIGPNGAGKTTVFNMIAGVFEPDEGRIE 64

Query: 70  FDGEPIQQLQPHQIAQQGMVRTFQVARTLSRLSVLENMLLAAQKQTGENFWQVQLQPQVV 129
            +G  +  L+P Q+ + G+ RTFQ+ +    +SV EN+L+ A + T              
Sbjct: 65  MEGASLVGLRPDQVCRTGIGRTFQLVKPFGNISVEENVLIGALRWT-------------- 110

Query: 130 VKEEKQLQEQAMFLLESVGLAKKAYEYAGGLSGGQRKLLEMGRALMTNPKLILLDEPAAG 189
             +  Q + +A  +LE +GLA K  + A GL+   RK LE+ RAL T PKL+LLDE  AG
Sbjct: 111 -HDVDQARRRAREVLELLGLADKRRQMARGLTLPDRKCLEVARALATGPKLLLLDEVMAG 169

Query: 190 VNPRLIDDICDRILTWNRQDGMTFLIIEHNMDVIMSLCDRVWVLAEGQNLADGTPAEIQT 249
           + P   D + +     NR+ G+T ++IEH M  +M+L  RV V+  G+ + +G P E+  
Sbjct: 170 LRPAETDRMVETFRRLNRETGLTIVLIEHVMRAVMALSQRVVVINTGKPVCEGAPEEVVR 229

Query: 250 NSQVLEAYLGK 260
           + +VLE YLG+
Sbjct: 230 DPRVLECYLGQ 240


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: 159
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: 243
Length adjustment: 24
Effective length of query: 236
Effective length of database: 219
Effective search space:    51684
Effective search space used:    51684
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: 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