Alignments for a candidate for HSERO_RS03640 in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for HSERO_RS03640 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:D8IZC7
         (521 letters)



>FitnessBrowser__Cup4G11:RR42_RS04800
          Length = 529

 Score =  279 bits (714), Expect = 2e-79
 Identities = 173/507 (34%), Positives = 283/507 (55%), Gaps = 19/507 (3%)

Query: 1   MTQTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQ 60
           ++ TP L +  I K +    A  D+ L + PGEIHA++GENGAGKSTLMK++ G   PD 
Sbjct: 3   LSTTPRLALAHISKRYPGVTANDDVSLVVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDA 62

Query: 61  GEILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSEL--RTRLGLIDHA 118
           G++  +G   A+ +P  +R  GI +++Q  ++   ++VA N+ +G     +T  G     
Sbjct: 63  GDMHFNGARAAIHNPHDARNLGIAMVFQHFSLFDTLTVAENIALGLPRGSKTAAGSPHAG 122

Query: 119 AMRSRTDAVLRQLGAGFGASDLAGR----LSIAEQQQVEIARALVHRSRIVIMDEPTAAL 174
               +    +R+    +G      R    LS+ E+Q+VEI RAL+ + +++I+DEPT+ L
Sbjct: 123 TNMKQLAEQIRETALRYGLPLEPNRHVHTLSVGERQRVEIVRALLAKPQLLILDEPTSVL 182

Query: 175 SERETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSER 234
           + +  + LF  +R+L  EG +I+YISH++ E+  L    TV+R G   G     +  +  
Sbjct: 183 TPQAVQTLFITLRQLAAEGTSILYISHKLDEIRELCHSATVMRMGRVTGVCDPRQESAAS 242

Query: 235 IVQMMVGRSLSEFYQHQ------RIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVL 288
           + ++M+G       + Q      R+A  + +   +      LAG      S D+RAGE++
Sbjct: 243 LSRLMIGGEPPREARVQTEPGVCRLAVRELSLPRSHAFATELAG-----ISLDLRAGEIV 297

Query: 289 GFAGLVGAGRTELARLLFGADPRSGGD-ILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQG 347
           G AG+ G G+ EL   L G D R+  D I L+ +PV     R   RAG+A+VPE+R G+G
Sbjct: 298 GIAGVSGNGQQELLAALSGEDVRAARDAITLDNKPVGKLDARQRRRAGLAFVPEERLGRG 357

Query: 348 LFLQMAVAANATMNVASR-HTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGN 406
               M++AAN  ++  S  + + G++  ++  G+A+A I RL VK + P      LSGGN
Sbjct: 358 AVPGMSLAANILLSHQSAPYVQRGMISPKAAAGLAQAVIARLRVKASGPHALAKSLSGGN 417

Query: 407 QQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIG 466
            QK ++ R +E  PKVLI+ +PT GVD+ A ++I+  +  L + G A++V+S EL E+  
Sbjct: 418 LQKFIVGREIESGPKVLIVAQPTWGVDVGAAAQIHNELLALKATGCALLVVSEELDELFA 477

Query: 467 ICDRVLVMREGMITGELAGAAITQENI 493
           ICDR+ V+ +G ++  +     T+E +
Sbjct: 478 ICDRLHVIAKGRLSPSIPTRDATREQV 504



 Score = 84.7 bits (208), Expect = 7e-21
 Identities = 69/233 (29%), Positives = 106/233 (45%), Gaps = 9/233 (3%)

Query: 279 SFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAY 338
           S  V  GE+    G  GAG++ L +++FGA     GD+   G    I  P  A   GIA 
Sbjct: 28  SLVVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDAGDMHFNGARAAIHNPHDARNLGIAM 87

Query: 339 VPEDRKGQGLFLQMAVAANATMNVA-SRHTRLGLVRS----RSLGGVARAAIQRLNVKVA 393
           V +      LF  + VA N  + +     T  G   +    + L    R    R  + + 
Sbjct: 88  VFQHFS---LFDTLTVAENIALGLPRGSKTAAGSPHAGTNMKQLAEQIRETALRYGLPL- 143

Query: 394 HPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVA 453
            P   V  LS G +Q+V + R L   P++LILDEPT  +   A   ++  + +LA++G +
Sbjct: 144 EPNRHVHTLSVGERQRVEIVRALLAKPQLLILDEPTSVLTPQAVQTLFITLRQLAAEGTS 203

Query: 454 VVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTA 506
           ++ IS +L E+  +C    VMR G +TG       +  ++ RL      PR A
Sbjct: 204 ILYISHKLDEIRELCHSATVMRMGRVTGVCDPRQESAASLSRLMIGGEPPREA 256


Lambda     K      H
   0.320    0.135    0.378 

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: 683
Number of extensions: 44
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: 521
Length of database: 529
Length adjustment: 35
Effective length of query: 486
Effective length of database: 494
Effective search space:   240084
Effective search space used:   240084
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