GapMind for catabolism of small carbon sources

 

Alignments for a candidate for livG 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::Q8DQH8
         (254 letters)



>NCBI__GCF_000284315.1:WP_232502519.1
          Length = 588

 Score =  110 bits (274), Expect = 9e-29
 Identities = 76/244 (31%), Positives = 123/244 (50%), Gaps = 25/244 (10%)

Query: 4   LEVKQLTKHFGGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEGTVTLD 63
           +EV+ L ++F    AV ++T  + +GE+ GL+G NGAGKTT F +L G+ EP+ G +   
Sbjct: 342 IEVENLDRYFDSFKAVNNLTFHVKKGEVFGLLGANGAGKTTTFRMLAGLLEPTAGKL--- 398

Query: 64  GHLLNGKSPYKIASLG---LGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRLPA 120
             ++ G+   K+A+     +G   Q   L+  LTV  N+           +F S     A
Sbjct: 399 --IVAGEDVRKVAAQARGKIGYMAQKFSLYSQLTVFQNL-----------IFYS----SA 441

Query: 121 FYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEPAA 180
           +  S    K K  + L  F+L+      +  L  G ++RL +  AL  EP ILFLDEP +
Sbjct: 442 YGLSGTLQKEKIQDSLNFFELEPYKNVSSGILPLGFRQRLALSCALIHEPSILFLDEPTS 501

Query: 181 GMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDEIK 240
           G++P    E   +I  +     +++++  H M    E  +R+ ++  G L+A G+P EIK
Sbjct: 502 GVDPNARREFWHIINALA-TVGVSVLVTTHFME-EAEYCDRLLIMAQGALLAMGSPAEIK 559

Query: 241 TNKR 244
              R
Sbjct: 560 EKTR 563



 Score =  102 bits (254), Expect = 2e-26
 Identities = 75/242 (30%), Positives = 125/242 (51%), Gaps = 22/242 (9%)

Query: 3   LLEVKQLTKHF----GGLTAVGDVTLELNEGELVGLIGPNGAGKTTLFNLLTGVYEPSEG 58
           L+ V +LTK F    G +TA+  ++  L +G + GLIGP+GAGKTTL  LL+G+  P  G
Sbjct: 10  LITVNELTKTFPSPRGIVTALDKISFSLKKGSITGLIGPDGAGKTTLMRLLSGLLWPDGG 69

Query: 59  TVTLDGHLLNGKSPYKIASLGLGRTFQNIRLFKDLTVLDNVLIAFGNHHKQHVFTSFLRL 118
            + + G+    K+P  +    LG   Q   L++DL+V +N+           ++ +   +
Sbjct: 70  DIRIMGN-DPSKAPLSVQG-SLGYMPQKFGLYEDLSVQENL----------DLYANLQGV 117

Query: 119 PAFYKSEKELKAKALELLKIFDLDGDAETLAKNLSYGQQRRLEIVRALATEPKILFLDEP 178
           P      KEL A    LL +  L    + LA  LS G +++L +  +L  +P IL LDEP
Sbjct: 118 PK--DRRKELYA---PLLSMTGLSPFQKRLAGQLSGGMKQKLGVACSLVHQPPILLLDEP 172

Query: 179 AAGMNPQETAELTELIRRIKDEFKITIMLIEHDMNLVMEVTERIYVLEYGRLIAQGTPDE 238
             G++P    EL E++R++  E   T+ +    ++   E  + I +L  G+++  G P+ 
Sbjct: 173 TVGVDPVSRRELWEILRKLVSESGATLFVSTSYLD-EAERCDEILILYNGKVLGSGPPES 231

Query: 239 IK 240
            +
Sbjct: 232 FR 233


Lambda     K      H
   0.319    0.139    0.385 

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: 342
Number of extensions: 18
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: 254
Length of database: 588
Length adjustment: 30
Effective length of query: 224
Effective length of database: 558
Effective search space:   124992
Effective search space used:   124992
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: 50 (23.9 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