GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Magnetospirillum magneticum AMB-1

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_043744393.1 AMB_RS12355 ABC transporter ATP-binding protein

Query= uniprot:D8J1T6
         (255 letters)



>NCBI__GCF_000009985.1:WP_043744393.1
          Length = 243

 Score =  182 bits (461), Expect = 7e-51
 Identities = 98/249 (39%), Positives = 154/249 (61%), Gaps = 16/249 (6%)

Query: 5   LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64
           LL +  + K F GL+A++GV  ++  G++  LIGPNGAGKTT FN+I G+++PD G  E+
Sbjct: 6   LLLVEGLVKNFRGLRAVDGVSFSVAAGEVVALIGPNGAGKTTVFNMIAGVFEPDEGRIEM 65

Query: 65  DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124
           +G       P +V + GI RTFQ ++ FG ++V ENV++G  +R   +V  A        
Sbjct: 66  EGASLVGLRPDQVCRTGIGRTFQLVKPFGNISVEENVLIGA-LRWTHDVDQA-------- 116

Query: 125 EEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGM 184
                 R +++++L+ +G+    ++ AR L+  D++ LE+ARALAT P+LL LDE  AG+
Sbjct: 117 ------RRRAREVLELLGLADKRRQMARGLTLPDRKCLEVARALATGPKLLLLDEVMAGL 170

Query: 185 NATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQKN 243
              E   + E   ++  E G TI+LIEH ++ +M L  R+ V++ GKP+ EG P +V ++
Sbjct: 171 RPAETDRMVETFRRLNRETGLTIVLIEHVMRAVMALSQRVVVINTGKPVCEGAPEEVVRD 230

Query: 244 PAVIEAYLG 252
           P V+E YLG
Sbjct: 231 PRVLECYLG 239


Lambda     K      H
   0.320    0.138    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: 179
Number of extensions: 8
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: 255
Length of database: 243
Length adjustment: 24
Effective length of query: 231
Effective length of database: 219
Effective search space:    50589
Effective search space used:    50589
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: 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