GapMind for catabolism of small carbon sources

 

Aligments for a candidate for H281DRAFT_01113 in Pseudomonas simiae WCS417

Align deoxynucleoside transporter, ATPase component (characterized)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein

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



>lcl|FitnessBrowser__WCS417:GFF2332 PS417_11890 D-ribose transporter
           ATP-binding protein
          Length = 517

 Score =  327 bits (838), Expect = 6e-94
 Identities = 186/508 (36%), Positives = 291/508 (57%), Gaps = 15/508 (2%)

Query: 3   QQEVSSAPLSQP-------FLEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKS 55
           Q  VS  P  QP        LE+V + K F GV AL  V L  + G +  L+GENG GKS
Sbjct: 4   QATVSQPPSLQPQTLEEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKS 63

Query: 56  TLIKIISGAQPPDEGQLVIEGVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTS 115
           TL+KII+G   PD G++ + G P    + L A  AGI  ++Q+L+L+P+MS+AEN+ +  
Sbjct: 64  TLMKIIAGIYQPDAGEIRLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGR 123

Query: 116 ELATHEGRLARTFDRRVLAATAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIA 175
           E            + R +    A  L  + +  + E Q   +  L +A RQ+V IA+A++
Sbjct: 124 EQLNS----LHMVNHREMHRCTAELLARLRINLDPEEQ---VGNLSIAERQMVEIAKAVS 176

Query: 176 SEAKFVIMDEPTTSLTQKEVDNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDG 235
            ++  +IMDEPT+++T+KEV +L +++A+L++QG  +++++HK++E +AI  EV V RDG
Sbjct: 177 YDSDILIMDEPTSAITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDG 236

Query: 236 QKMAQGPIAEFTKAQISELMTGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLH 295
             +            +  +M GR LS           D++L VR  T  G F DVSF LH
Sbjct: 237 HYIGLQRADSMNSDSLISMMVGRELSQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLH 296

Query: 296 GGEILGVTGLLDSGRNELARALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDR 355
            GEILG+ GL+ SGR  +A  + G+ P+ SG + LDG+ + +  P  A       + EDR
Sbjct: 297 AGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDR 356

Query: 356 LNEGLFLDKPIRDNVITAMISSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSL 415
              GLF    + +N+  A++       G I +   +AL E   K+L++ TP +++ + +L
Sbjct: 357 KLSGLFPCLSVLENMEMAVLPHYTGN-GFIQQKALRALCEDMCKKLRVKTPSLEQCIDTL 415

Query: 416 SGGNQQRVLIGRWLAIDPRVLILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLP 475
           SGGNQQ+ L+ RWL  +PR+LIL  PT G+DVG+K  IYR++  L+  G+ +I+IS +LP
Sbjct: 416 SGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELP 475

Query: 476 ELLQNCDRILMMKKGHVSAEYRADELSE 503
           E+L   DR+++M +G +       E ++
Sbjct: 476 EVLGMSDRVMVMHEGELMGTLDRSEATQ 503



 Score = 70.5 bits (171), Expect = 1e-16
 Identities = 56/242 (23%), Positives = 110/242 (45%), Gaps = 10/242 (4%)

Query: 267 ESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELARALAGVAPAQSG 326
           E  +  +IV   +GF      +DV  ++  G +L + G   +G++ L + +AG+    +G
Sbjct: 19  EEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAG 78

Query: 327 DVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMISSLRDRFGQID 386
           ++ L G+ I   TP  A++  I  + ++ LN  L     I +N+        R++   + 
Sbjct: 79  EIRLRGKPIVFETPLAAQKAGIAMIHQE-LN--LMPHMSIAENIWIG-----REQLNSLH 130

Query: 387 RTRAQALAEQTVKELQIATPGVD--KPVQSLSGGNQQRVLIGRWLAIDPRVLILHGPTVG 444
               + +   T + L      +D  + V +LS   +Q V I + ++ D  +LI+  PT  
Sbjct: 131 MVNHREMHRCTAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSA 190

Query: 445 VDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVSAEYRADELSEA 504
           +       ++ I+  L  +G GI+ I+  + E+    D + + + GH     RAD ++  
Sbjct: 191 ITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSD 250

Query: 505 DL 506
            L
Sbjct: 251 SL 252



 Score = 65.9 bits (159), Expect = 3e-15
 Identities = 53/229 (23%), Positives = 105/229 (45%), Gaps = 8/229 (3%)

Query: 32  RGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIEGVPHARLSALEALAAG 91
           + VS     G+I  + G  G G++ + + I G  P   GQ+ ++G          A+  G
Sbjct: 289 KDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKG 348

Query: 92  IETVYQDLSL---LPNMSVAENVALTSELATHEGRLARTFDRRVLAATAARALEAVGLPG 148
              + +D  L    P +SV EN+ + + L  + G       ++ L A      + + +  
Sbjct: 349 FALLTEDRKLSGLFPCLSVLENMEM-AVLPHYTGN--GFIQQKALRALCEDMCKKLRVKT 405

Query: 149 NSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEVDNLIAVLANLRAQ 208
            S  Q   I+ L    +Q   +AR + +  + +I+DEPT  +       +  ++A L ++
Sbjct: 406 PSLEQC--IDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASE 463

Query: 209 GVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELMTG 257
           G+ V+ +S +L E   +   V+V+ +G+ M     +E T+ ++ +L +G
Sbjct: 464 GMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512


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: 562
Number of extensions: 32
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
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, the preprint on GapMind for carbon sources, 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