Alignments for a candidate for HSERO_RS05250 in Cupriavidus basilensis 4G11

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_RS04800 RR42_RS04800 ABC transporter

Query= uniprot:D8J111
         (520 letters)



>FitnessBrowser__Cup4G11:RR42_RS04800
          Length = 529

 Score =  273 bits (697), Expect = 1e-77
 Identities = 170/501 (33%), Positives = 272/501 (54%), Gaps = 11/501 (2%)

Query: 18  SSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSG 77
           S+ P +AL ++ KR+PGV A D+    +A GE+HA++GENGAGKSTLMKI+ G  + D+G
Sbjct: 4   STTPRLALAHISKRYPGVTANDDVSLVVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDAG 63

Query: 78  DILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIG--REPRKAMG---LFI 132
           D+  +G    I  P  A+ LGI ++ Q  +L + L+ A+NI +G  R  + A G      
Sbjct: 64  DMHFNGARAAIHNPHDARNLGIAMVFQHFSLFDTLTVAENIALGLPRGSKTAAGSPHAGT 123

Query: 133 DEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALN 192
           +  +L  Q      R  L ++P+  V  L+V  +Q VEI +AL    ++LI+DEPT+ L 
Sbjct: 124 NMKQLAEQIRETALRYGLPLEPNRHVHTLSVGERQRVEIVRALLAKPQLLILDEPTSVLT 183

Query: 193 NAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTI 252
              +  LF  +R L A+G  I+YISHK+DE+R++    +VMR G+       ++ S  ++
Sbjct: 184 PQAVQTLFITLRQLAAEGTSILYISHKLDEIRELCHSATVMRMGRVTGVCDPRQESAASL 243

Query: 253 ISMMVGRALDGEQRIPPDTSRNDVVLEVRGLNRGRA----IRDVSFTLRKGEILGFAGLM 308
             +M+G     E R+  +     + +    L R  A    +  +S  LR GEI+G AG+ 
Sbjct: 244 SRLMIGGEPPREARVQTEPGVCRLAVRELSLPRSHAFATELAGISLDLRAGEIVGIAGVS 303

Query: 309 GAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPA-DAVAHGIGYLSEDRKHFGLAVGMD 367
           G G+ E+  A+ G D   A + I    K V K  A      G+ ++ E+R   G   GM 
Sbjct: 304 GNGQQELLAALSGEDVRAARDAITLDNKPVGKLDARQRRRAGLAFVPEERLGRGAVPGMS 363

Query: 368 VQANIALSSMGR-FTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVI 426
           + ANI LS     + + G +  +A    AQ  + +L +K       A+ LSGGN QK ++
Sbjct: 364 LAANILLSHQSAPYVQRGMISPKAAAGLAQAVIARLRVKASGPHALAKSLSGGNLQKFIV 423

Query: 427 AKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVL 486
            + +     +L   +PT G+DVGA ++I+  L AL   G A++++S EL E+  +  R+ 
Sbjct: 424 GREIESGPKVLIVAQPTWGVDVGAAAQIHNELLALKATGCALLVVSEELDELFAICDRLH 483

Query: 487 VMCEGRITGELARADATQEKI 507
           V+ +GR++  +   DAT+E++
Sbjct: 484 VIAKGRLSPSIPTRDATREQV 504



 Score = 77.0 bits (188), Expect = 2e-18
 Identities = 61/237 (25%), Positives = 109/237 (45%), Gaps = 26/237 (10%)

Query: 38  LDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGD-ILLDGKPVEITEPRQAQA 96
           L     +L AGE+  + G +G G+  L+  LSG   R + D I LD KPV   + RQ + 
Sbjct: 284 LAGISLDLRAGEIVGIAGVSGNGQQELLAALSGEDVRAARDAITLDNKPVGKLDARQRRR 343

Query: 97  LGIGIIHQEL---NLMNHLSAAQNIFIGRE-----------PRKAMGLFIDEDELNRQAA 142
            G+  + +E      +  +S A NI +  +           P+ A GL          A 
Sbjct: 344 AGLAFVPEERLGRGAVPGMSLAANILLSHQSAPYVQRGMISPKAAAGL----------AQ 393

Query: 143 AIFARMRLDMD-PSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201
           A+ AR+R+    P      L+    Q   + + +    +VLI+ +PT  ++    A++  
Sbjct: 394 AVIARLRVKASGPHALAKSLSGGNLQKFIVGREIESGPKVLIVAQPTWGVDVGAAAQIHN 453

Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258
            +  L+A G  ++ +S ++DEL  I DR+ V+  G+   ++P ++ + + +   M G
Sbjct: 454 ELLALKATGCALLVVSEELDELFAICDRLHVIAKGRLSPSIPTRDATREQVGLWMSG 510


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: 620
Number of extensions: 38
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 520
Length of database: 529
Length adjustment: 35
Effective length of query: 485
Effective length of database: 494
Effective search space:   239590
Effective search space used:   239590
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.

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources