GapMind for catabolism of small carbon sources

 

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

Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate WP_011383886.1 AMB_RS07455 ABC transporter ATP-binding protein

Query= SwissProt::Q9F9B0
         (260 letters)



>NCBI__GCF_000009985.1:WP_011383886.1
          Length = 261

 Score =  117 bits (292), Expect = 3e-31
 Identities = 78/249 (31%), Positives = 123/249 (49%), Gaps = 27/249 (10%)

Query: 1   MAQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDE 60
           M+Q   L+ RGL K YG V A+   DFDL PGEILA+IG NGAGKS+    ++G   P  
Sbjct: 1   MSQNQTLSVRGLSKNYGGVAAVTNVDFDLAPGEILALIGPNGAGKSTCFNMLNGQFPPTA 60

Query: 61  GEIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKW--- 117
           G I+L G+ +  + P E  + G+   +Q  A   ++++ +N+ +        +   W   
Sbjct: 61  GSIKLFGEELVGKKPREIWRLGVGRTFQITATFGSMTVLENVQMALISFHNRLRALWPFA 120

Query: 118 --------FRSLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFG 169
                   F+ L+   ME QA               ++    L+ G  + V +A A A  
Sbjct: 121 GGLYQDEAFQLLELVGMEAQA---------------SRPCSVLAYGDLKRVELAVALANA 165

Query: 170 SKVVIMDEPTAALGVKESRRVLELILD-VRRRGLPIVLISHNMPHVFEVADRIHIHRLGR 228
            K+++MDEPTA +  KE   +++L  D VR RG+ ++   H+M  VF  A+RI +   G 
Sbjct: 166 PKLLLMDEPTAGMAPKERIELMQLTADIVRERGISVLFTEHDMDVVFTHANRIMVLSRGH 225

Query: 229 RLCVINPKD 237
            +    P++
Sbjct: 226 VVAEGKPQE 234


Lambda     K      H
   0.321    0.136    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: 144
Number of extensions: 4
Number of successful extensions: 3
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: 261
Length adjustment: 25
Effective length of query: 235
Effective length of database: 236
Effective search space:    55460
Effective search space used:    55460
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: 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