GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS00895 in Alkalihalobacterium alkalinitrilicum DSM 22532

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein

Query= uniprot:D8J1T6
         (255 letters)



>NCBI__GCF_002019605.1:WP_078427103.1
          Length = 509

 Score =  130 bits (328), Expect = 4e-35
 Identities = 74/228 (32%), Positives = 130/228 (57%), Gaps = 12/228 (5%)

Query: 5   LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64
           +++++D+ K F G+ A + V + +++G+I+ L+G NGAGK+T  NV+ GLYQP+ G   +
Sbjct: 4   VIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEILV 63

Query: 65  DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124
            GKP   + P+   + GI    Q+  L  + TV EN+++G     +    G +   KAA+
Sbjct: 64  KGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILG----KEPTAGGKINIKKAAK 119

Query: 125 EEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGM 184
             E   ++        + +  +AK   + +S G Q+R+EI + L    ++L  DEP A +
Sbjct: 120 AVETISKQYG------LAVDPYAK--IQDISVGMQQRVEILKTLYRGAEILIFDEPTAAL 171

Query: 185 NATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPI 232
              E   L +++ K+ +EGK+I+LI H +K +M +C+R TV+  G+ I
Sbjct: 172 TPQEITELIQIMKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGI 219



 Score = 89.7 bits (221), Expect = 1e-22
 Identities = 64/234 (27%), Positives = 122/234 (52%), Gaps = 13/234 (5%)

Query: 5   LLKIRD-VSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFE 63
           +L+I+D V K    + A+N + + +  G+I G+ G +G G+T     ITGL +P  G  +
Sbjct: 256 VLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGGNIQ 315

Query: 64  LDGKPYSPSAPHEVAKAGIARTFQNIRLFG---EMTVLENVMVGCHVRTKQNVFGAVFRH 120
           L+G+  +   P ++  AG+    Q+    G   + TV EN+++  + +   +  G +  +
Sbjct: 316 LNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYYQKPYSTSGVLNFN 375

Query: 121 KAAREEEAAIREKSQKLLDFVGIGQFAKRT-ARHLSYGDQRRLEIARALATDPQLLALDE 179
           +        I +K+ +L++   +   ++ T AR LS G+Q++  IAR +   P LL   +
Sbjct: 376 E--------IYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQ 427

Query: 180 PAAGMNATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIA 233
           P  G++      +   LVK + +GK +LLI  ++  ++ + +RI V+  GK +A
Sbjct: 428 PTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVA 481


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: 309
Number of extensions: 14
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 255
Length of database: 509
Length adjustment: 29
Effective length of query: 226
Effective length of database: 480
Effective search space:   108480
Effective search space used:   108480
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: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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