GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HSERO_RS05250 in Cupriavidus basilensis 4G11

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate RR42_RS30800 RR42_RS30800 sugar ABC transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__Cup4G11:RR42_RS30800
          Length = 530

 Score =  272 bits (695), Expect = 3e-77
 Identities = 170/494 (34%), Positives = 272/494 (55%), Gaps = 24/494 (4%)

Query: 21  PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80
           P++ L  + KRF  ++A D+   EL  GEV AL+GENGAGKSTL+ IL G Y  D+G + 
Sbjct: 4   PILRLAGITKRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVE 63

Query: 81  LDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQ 140
           +DG+P+   +PR A   GIG++HQ   L ++LS   NI +G +P     L  D      +
Sbjct: 64  VDGQPLPPGQPRAALTAGIGMVHQHFTLADNLSVLDNIMLGTQPLWQWRL--DGHAARGK 121

Query: 141 AAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELF 200
             A+  R  L + P   VGEL+V  +Q VEI KAL   +RVLI+DEPTA L   E   LF
Sbjct: 122 VLALAERFGLAVRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLF 181

Query: 201 RIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRA 260
             +  L A+G+ +++ISHK+DE+ +++DR++V+R GK +A     +T+   +  +MVGR 
Sbjct: 182 STLAQLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMVGRV 241

Query: 261 LDGEQRIPPDTSRND---------VVLE---VRGLNRGRAIRDVSFTLRKGEILGFAGLM 308
           +   +R+   ++ +          + LE    R  N    +R+VS  +R GEI+G AG+ 
Sbjct: 242 VAMPERVARRSAEDGANGNAAPPVLALEHVGARAANGRALLREVSLQVRAGEIVGIAGVS 301

Query: 309 GAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDV 368
           G G+  +A    G      G I +  GK +   P   +  G+  + EDR   G+   + V
Sbjct: 302 GNGQAALAELASGMLEASEGRITL-AGKPMSAKPRAWIGAGVARVPEDRHAIGVVGDLAV 360

Query: 369 QANIALSSMG--RFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVI 426
             N     +   RF+R G + + A +  A+  V +  ++T  ++  AR +SGGN QK+++
Sbjct: 361 WENAVSEQLSEPRFSRWGVIRRAAAQRFARDLVARFDVRTAGIDVPARTMSGGNMQKLIL 420

Query: 427 AKWLLRDCD-----ILFFDEPTRGIDVGAKSEI-YKLLDALAEQGKAIVMISSELPEVLR 480
            + L    +     ++   +PT G+D+GA + +  +LLDA A +G A+++IS +L E+  
Sbjct: 421 GRALSVRGEGSAPRLVVASQPTWGLDIGAVAYVRARLLDA-AREGAAVLLISEDLDELHA 479

Query: 481 MSHRVLVMCEGRIT 494
           ++ R+ VM  G +T
Sbjct: 480 LADRIAVMHAGHLT 493



 Score = 94.0 bits (232), Expect = 1e-23
 Identities = 68/230 (29%), Positives = 112/230 (48%), Gaps = 10/230 (4%)

Query: 291 DVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGI 350
           D+S  L++GE+L   G  GAG++ +   +FG    +AG + + G       P  A+  GI
Sbjct: 23  DISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVEVDGQPLPPGQPRAALTAGI 82

Query: 351 GYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVE 410
           G + +   HF LA  + V  NI L +   +     +D  A R        +  +   +V 
Sbjct: 83  GMVHQ---HFTLADNLSVLDNIMLGTQPLWQ--WRLDGHAARGKVLALAERFGL---AVR 134

Query: 411 QQARL--LSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAI 468
            QAR+  LS G +Q++ I K L R   +L  DEPT  +       ++  L  L  +G ++
Sbjct: 135 PQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLFSTLAQLIAEGLSV 194

Query: 469 VMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLATQRESAV 518
           + IS +L EVLR+S R+ V+  G++    A A  T+ ++ +L   R  A+
Sbjct: 195 IFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMVGRVVAM 244



 Score = 75.1 bits (183), Expect = 6e-18
 Identities = 67/262 (25%), Positives = 122/262 (46%), Gaps = 23/262 (8%)

Query: 14  ASSSSSVPVIALRNVCKRFP-GVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVY 72
           A+ +++ PV+AL +V  R   G   L     ++ AGE+  + G +G G++ L ++ SG+ 
Sbjct: 257 ANGNAAPPVLALEHVGARAANGRALLREVSLQVRAGEIVGIAGVSGNGQAALAELASGML 316

Query: 73  QRDSGDILLDGKPVEITEPRQAQALGIGIIHQE---LNLMNHLSAAQNIFIGR--EPRKA 127
           +   G I L GKP+   +PR     G+  + ++   + ++  L+  +N    +  EPR  
Sbjct: 317 EASEGRITLAGKPMS-AKPRAWIGAGVARVPEDRHAIGVVGDLAVWENAVSEQLSEPR-- 373

Query: 128 MGLFIDEDELNRQAAAIFAR---MRLDMDPS---TPVGELTVARQQMVEIAKALSFDS-- 179
              F     + R AA  FAR    R D+  +    P   ++    Q + + +ALS     
Sbjct: 374 ---FSRWGVIRRAAAQRFARDLVARFDVRTAGIDVPARTMSGGNMQKLILGRALSVRGEG 430

Query: 180 ---RVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDG 236
              R+++  +PT  L+   +A +   + D   +G  ++ IS  +DEL  +ADR++VM  G
Sbjct: 431 SAPRLVVASQPTWGLDIGAVAYVRARLLDAAREGAAVLLISEDLDELHALADRIAVMHAG 490

Query: 237 KYIATVPMQETSMDTIISMMVG 258
                 P    ++  +   M G
Sbjct: 491 HLTEARPTAAWTLGELGLAMAG 512


Lambda     K      H
   0.320    0.135    0.372 

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: 648
Number of extensions: 33
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: 3
Length of query: 520
Length of database: 530
Length adjustment: 35
Effective length of query: 485
Effective length of database: 495
Effective search space:   240075
Effective search space used:   240075
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 (21.8 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 (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