GapMind for catabolism of small carbon sources

 

Aligments for a candidate for H281DRAFT_01113 in Herbaspirillum seropedicae SmR1

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate HSERO_RS05090 HSERO_RS05090 sugar ABC transporter ATP-binding protein

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



>lcl|FitnessBrowser__HerbieS:HSERO_RS05090 HSERO_RS05090 sugar ABC
           transporter ATP-binding protein
          Length = 501

 Score =  669 bits (1726), Expect = 0.0
 Identities = 331/494 (67%), Positives = 401/494 (81%)

Query: 20  GVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPH 79
           G+HKRF GVHALRGV L+   G+IYHLLGENGCGKSTLIKII+GAQPP EG++ I+G   
Sbjct: 3   GIHKRFAGVHALRGVDLTIHAGEIYHLLGENGCGKSTLIKIIAGAQPPSEGEIYIQGQRV 62

Query: 80  ARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAATAAR 139
           A L+ L +L+ GIETVYQDLSLLPNMSVAENVAL+ +L  H+GRLAR FDR  L  TAAR
Sbjct: 63  AELTPLASLSLGIETVYQDLSLLPNMSVAENVALSEQLVHHQGRLARLFDRHALNQTAAR 122

Query: 140 ALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLI 199
           AL AV LP +++F  T +++LP+ATRQL+AIARAIA+ A+ VIMDEPTTSLTQKEVD L+
Sbjct: 123 ALRAVNLPADADFLDTRVDELPIATRQLIAIARAIATSARMVIMDEPTTSLTQKEVDALV 182

Query: 200 AVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTGRH 259
            V+  LRA GV VLFVSHKLDEC+AIGG+ IV RDG+K+AQGPI +FTKAQ+ +LMTG+ 
Sbjct: 183 KVINGLRANGVAVLFVSHKLDECFAIGGQAIVFRDGEKVAQGPIQQFTKAQLGQLMTGKQ 242

Query: 260 LSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELARALAG 319
           LS ERYR  A     +++VR   R G F DVSF L  GEILG+TGLLDSGRNELA ALAG
Sbjct: 243 LSQERYRVDAQLHKPLMEVRALGRHGAFEDVSFALRQGEILGITGLLDSGRNELALALAG 302

Query: 320 VAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLR 379
           V PA++G + L+GQ ++LR P DA  H IGYVPEDR++EGLFLDK IRDN++T ++  LR
Sbjct: 303 VEPARAGQITLEGQPLSLRNPGDAITHGIGYVPEDRISEGLFLDKSIRDNIVTTILRKLR 362

Query: 380 DRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRVLILH 439
            +FG +D    Q  +  TV++LQIATP VD+PVQSLSGGNQQRVLIGRWLAI+PRVLILH
Sbjct: 363 GKFGALDAAACQRFSTDTVRQLQIATPDVDRPVQSLSGGNQQRVLIGRWLAINPRVLILH 422

Query: 440 GPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRAD 499
           GPTVGVDVGSKDIIYRI+Q L+QRG+G+ILISDDLPELLQNCD +L+MK+G +   Y  +
Sbjct: 423 GPTVGVDVGSKDIIYRIIQDLAQRGLGVILISDDLPELLQNCDNLLLMKRGRIVRRYAVE 482

Query: 500 ELSEADLYHALLSE 513
            L+E++L+H L+SE
Sbjct: 483 GLAESELFHDLVSE 496


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: 790
Number of extensions: 27
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: 515
Length of database: 501
Length adjustment: 34
Effective length of query: 481
Effective length of database: 467
Effective search space:   224627
Effective search space used:   224627
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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