GapMind for catabolism of small carbon sources

 

Alignments for a candidate for H281DRAFT_01113 in Paucidesulfovibrio gracilis DSM 16080

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein

Query= reanno::Burk376:H281DRAFT_01113
         (515 letters)



>NCBI__GCF_900167125.1:WP_078716498.1
          Length = 514

 Score =  215 bits (547), Expect = 4e-60
 Identities = 145/485 (29%), Positives = 251/485 (51%), Gaps = 20/485 (4%)

Query: 10  PLSQPFLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDE 69
           P   P + + G+ KRF  V A   +SL+   G++  LLGENG GKSTL+ +++G   PD 
Sbjct: 19  PQGIPLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDA 78

Query: 70  GQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFD 129
           G + ++G P    SA +A+ AGI  VYQ   L+ +M+VAENV L  E +       +   
Sbjct: 79  GTIALDGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQEGSFFLN--PKEMR 136

Query: 130 RRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTS 189
            RV   +    L+           +  +  L +  +Q V I + +  +++ +I DEPT  
Sbjct: 137 NRVQELSVRYGLDID--------PAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAV 188

Query: 190 LTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFT-K 248
           LT +E  +L   L  +  QG +++F+SHKL+E  A+  E+ +LR G+   +   +E T K
Sbjct: 189 LTPRETFHLFEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSK 248

Query: 249 AQISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDS 308
           A ++  M G+ +  E  RE+    D VL VR  T  G   D++F LH GE++ V G+  +
Sbjct: 249 ADLACRMVGKEVLLEVDREAMPHGDAVLQVRNLTGIG-LEDITFDLHQGEVVAVVGVAGN 307

Query: 309 GRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRD 368
           G+  L  A+ G+       + + G++        + ++ + Y+PEDRL  GL   + +  
Sbjct: 308 GQKALVEAICGLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRL--GLATCRNL-- 363

Query: 369 NVITAMISSLRDRFGQ---IDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLI 425
           N++  ++ + R  F +   +D+ +A     + +K+  I    +      LSGGN Q+ ++
Sbjct: 364 NLVDNLLLTTRQGFARGPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVL 423

Query: 426 GRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRIL 485
            R L   PR+++   PT G+D+ + + ++  +    +   GI+L++ DL E LQ  DR+ 
Sbjct: 424 ARELYRCPRLIVAEQPTQGLDIAATEQVWNHLLAAREMA-GILLVTGDLNEALQLADRVA 482

Query: 486 MMKKG 490
           ++ +G
Sbjct: 483 VIYRG 487



 Score = 72.0 bits (175), Expect = 5e-17
 Identities = 63/237 (26%), Positives = 113/237 (47%), Gaps = 14/237 (5%)

Query: 275 VLDVRGFT-RAGQF---SDVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSGDVLL 330
           ++ ++G T R G+     D+S  ++ G +  + G   +G++ L   LAG     +G + L
Sbjct: 24  LVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIAL 83

Query: 331 DGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRA 390
           DG+ +   +  DA    IG V +  +   L     + +NV+     S      ++ R R 
Sbjct: 84  DGKPVRFSSARDAIEAGIGMVYQHFM---LVESMTVAENVLLGQEGSFFLNPKEM-RNRV 139

Query: 391 QALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSK 450
           Q L+ +   ++  A       V  LS G +QRV I + L  D RVLI   PT  +     
Sbjct: 140 QELSVRYGLDIDPAAR-----VSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRET 194

Query: 451 DIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADEL-SEADL 506
             ++  + +++++G  I+ IS  L E+L   D I ++++G +  E+   E+ S+ADL
Sbjct: 195 FHLFEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADL 251


Lambda     K      H
   0.319    0.135    0.376 

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: 531
Number of extensions: 27
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 515
Length of database: 514
Length adjustment: 35
Effective length of query: 480
Effective length of database: 479
Effective search space:   229920
Effective search space used:   229920
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: 52 (24.6 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