GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livF in Leptospirillum ferrooxidans C2-3

Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate WP_232502519.1 LFE_RS09120 ATP-binding cassette domain-containing protein

Query= TCDB::Q8DQH7
         (236 letters)



>NCBI__GCF_000284315.1:WP_232502519.1
          Length = 588

 Score =  112 bits (281), Expect = 1e-29
 Identities = 73/227 (32%), Positives = 123/227 (54%), Gaps = 17/227 (7%)

Query: 4   LKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEFL 63
           ++VENL  ++   +AV +++F V +GEV  L+GANGAGKTT  R L+GL+ P++GK+   
Sbjct: 342 IEVENLDRYFDSFKAVNNLTFHVKKGEVFGLLGANGAGKTTTFRMLAGLLEPTAGKLIVA 401

Query: 64  GQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENL-------EMGAFLKKNREENQANL 116
           G++++K+ AQ    G +  + +   ++  LTV +NL        +   L+K + ++  N 
Sbjct: 402 GEDVRKVAAQ--ARGKIGYMAQKFSLYSQLTVFQNLIFYSSAYGLSGTLQKEKIQDSLN- 458

Query: 117 KKVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIF 176
                 F  LE  KN  +  L  G +Q LA+  AL+  P +L LDEP+ G+ P   +E +
Sbjct: 459 ------FFELEPYKNVSSGILPLGFRQRLALSCALIHEPSILFLDEPTSGVDPNARREFW 512

Query: 177 DIIQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKEL 223
            II  +   G +VL+      +A    DR  ++  G ++  G+  E+
Sbjct: 513 HIINALATVGVSVLVTTHFMEEA-EYCDRLLIMAQGALLAMGSPAEI 558



 Score =  112 bits (279), Expect = 2e-29
 Identities = 64/205 (31%), Positives = 112/205 (54%), Gaps = 2/205 (0%)

Query: 14  GMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIEFLGQEIQKMPAQ 73
           G++ A+  +SF + +G +  LIG +GAGKTT++R LSGL+ P  G I  +G +  K P  
Sbjct: 25  GIVTALDKISFSLKKGSITGLIGPDGAGKTTLMRLLSGLLWPDGGDIRIMGNDPSKAPLS 84

Query: 74  KIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVFSRFPRLEERKNQD 133
             V G L  +P+   ++  L+V ENL++ A L+   ++ +  L         L   + + 
Sbjct: 85  --VQGSLGYMPQKFGLYEDLSVQENLDLYANLQGVPKDRRKELYAPLLSMTGLSPFQKRL 142

Query: 134 AATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDIIQDIQKQGTTVLLIE 193
           A  LSGG +Q L +  +L+  P +LLLDEP++G+ P+  +E+++I++ +  +    L + 
Sbjct: 143 AGQLSGGMKQKLGVACSLVHQPPILLLDEPTVGVDPVSRRELWEILRKLVSESGATLFVS 202

Query: 194 QNANKALAISDRGYVLETGKIVLSG 218
            +        D   +L  GK++ SG
Sbjct: 203 TSYLDEAERCDEILILYNGKVLGSG 227


Lambda     K      H
   0.315    0.134    0.358 

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: 312
Number of extensions: 17
Number of successful extensions: 3
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: 236
Length of database: 588
Length adjustment: 30
Effective length of query: 206
Effective length of database: 558
Effective search space:   114948
Effective search space used:   114948
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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