GapMind for catabolism of small carbon sources

 

Aligments for a candidate for H281DRAFT_01113 in Pseudomonas fluorescens GW456-L13

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate PfGW456L13_3911 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

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



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3911 Ribose ABC
           transport system, ATP-binding protein RbsA (TC
           3.A.1.2.1)
          Length = 517

 Score =  298 bits (764), Expect = 2e-85
 Identities = 181/496 (36%), Positives = 280/496 (56%), Gaps = 11/496 (2%)

Query: 16  LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIE 75
           L V G+ K +     L G+ L+  RG++  L GENG GKSTL KII G   P  GQ+  +
Sbjct: 10  LSVSGIGKTYAQP-VLAGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQYQ 68

Query: 76  GVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAA 135
           G  +   S  +A A GI  V Q+L+LLP +SVAEN+ L + L +  G ++R    + L  
Sbjct: 69  GQDYRPGSRAQAEALGIRMVMQELNLLPTLSVAENLFLDN-LPSKGGWISR----KQLRK 123

Query: 136 TAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV 195
            A  A+  VGL        TL+ +L +  +Q+V IAR +  +   +I+DEPT  LT +EV
Sbjct: 124 AAIEAMAHVGLDAIDP--DTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREV 181

Query: 196 DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELM 255
           + L   +  L+++GV+++++SH+L+E   +   + VLRDG  +   P+A +   Q+  LM
Sbjct: 182 EMLFEQITRLQSRGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLM 241

Query: 256 TGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELAR 315
            GR L       +      VL V G +R+ +  DVSF++  GEI G++GL+ +GR EL R
Sbjct: 242 VGRELGEHIDMGARKIGAPVLTVNGLSRSDKVRDVSFEVRAGEIFGISGLIGAGRTELLR 301

Query: 316 ALAGVAPAQSGDVLLDG--QQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITA 373
            + G   A SG + L    Q I +R+P DA  H I  + EDR  EGL L + I  N+   
Sbjct: 302 LIFGADIADSGTIALGAPAQVINVRSPVDAVGHGIALITEDRKGEGLLLTQSIGANIALG 361

Query: 374 MISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDP 433
            +  +    G +D  + +ALA++ +  ++I + G  + V  LSGGNQQ+V+IGRWL  D 
Sbjct: 362 NMPGISGA-GFVDNDKERALAQRQIDAMRIRSSGPAQLVSELSGGNQQKVVIGRWLERDC 420

Query: 434 RVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVS 493
            VL+   PT G+DVG+K  IY ++  L+++G  ++++S DL EL+  CDRI ++  G + 
Sbjct: 421 SVLLFDEPTRGIDVGAKFDIYNLLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGSLI 480

Query: 494 AEYRADELSEADLYHA 509
             +  D  ++ +L  A
Sbjct: 481 DTFDRDSWTQDELLAA 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: 594
Number of extensions: 28
Number of successful extensions: 9
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: 517
Length adjustment: 35
Effective length of query: 480
Effective length of database: 482
Effective search space:   231360
Effective search space used:   231360
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.

Links

Downloads

Related tools

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