Alignments for a candidate for nupA in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Cupriavidus basilensis 4G11

Align Purine/cytidine ABC transporter ATP-binding protein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized)
to candidate RR42_RS04800 RR42_RS04800 ABC transporter

Query= TCDB::A2RKA7
         (506 letters)



>FitnessBrowser__Cup4G11:RR42_RS04800
          Length = 529

 Score =  329 bits (844), Expect = 1e-94
 Identities = 194/504 (38%), Positives = 292/504 (57%), Gaps = 11/504 (2%)

Query: 7   IQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVK 66
           + +  ++KR+    AND V+L +  GEIHA+LGENGAGKSTLM I+ G ++P  G++H  
Sbjct: 9   LALAHISKRYPGVTANDDVSLVVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDAGDMHFN 68

Query: 67  GKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIIL----GNEVTKG---INLDLKTA 119
           G    I +P  A NLGI MV QHF L D  TV ENI L    G++   G      ++K  
Sbjct: 69  GARAAIHNPHDARNLGIAMVFQHFSLFDTLTVAENIALGLPRGSKTAAGSPHAGTNMKQL 128

Query: 120 KKKILELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEIT 179
            ++I E + RYGL +EP+  +  +SVG++QRVEI++ L     +LI DEPT+VLTP  + 
Sbjct: 129 AEQIRETALRYGLPLEPNRHVHTLSVGERQRVEIVRALLAKPQLLILDEPTSVLTPQAVQ 188

Query: 180 ELMQIMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMV 239
            L   ++ L  EG SI+ I+HKLDEIR +    TV+R G+     +   ++   L+ LM+
Sbjct: 189 TLFITLRQLAAEGTSILYISHKLDEIRELCHSATVMRMGRVTGVCDPRQESAASLSRLMI 248

Query: 240 GRSVSFITEKAAAQPKDVVLEIKDLNIKESRG-SLKVKGLSLDVRAGEIVGVAGIDGNGQ 298
           G        +   +P    L +++L++  S   + ++ G+SLD+RAGEIVG+AG+ GNGQ
Sbjct: 249 GGEPP-REARVQTEPGVCRLAVRELSLPRSHAFATELAGISLDLRAGEIVGIAGVSGNGQ 307

Query: 299 TELVKAITGL-TKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAEN 357
            EL+ A++G   +    +I L NK +     R+     +  VPE+R   G V  M++A N
Sbjct: 308 QELLAALSGEDVRAARDAITLDNKPVGKLDARQRRRAGLAFVPEERLGRGAVPGMSLAAN 367

Query: 358 IALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIARE 417
           I L ++   P  + G +        A+ ++    V+ +G    A SLSGGN QK I+ RE
Sbjct: 368 ILL-SHQSAPYVQRGMISPKAAAGLAQAVIARLRVKASGPHALAKSLSGGNLQKFIVGRE 426

Query: 418 IDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIH 477
           I+  P +LIV+QPT G+DVGA   IH  L+  +  G A+LV+S ELDE+  + DR+ VI 
Sbjct: 427 IESGPKVLIVAQPTWGVDVGAAAQIHNELLALKATGCALLVVSEELDELFAICDRLHVIA 486

Query: 478 DGQIQGIVSPETTTKQELGILMVG 501
            G++   +     T++++G+ M G
Sbjct: 487 KGRLSPSIPTRDATREQVGLWMSG 510



 Score = 78.2 bits (191), Expect = 7e-19
 Identities = 65/231 (28%), Positives = 101/231 (43%), Gaps = 13/231 (5%)

Query: 278 LSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVG 337
           +SL V  GEI  V G +G G++ L+K I G  K D+G +  +        P       + 
Sbjct: 27  VSLVVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDAGDMHFNGARAAIHNPHDARNLGIA 86

Query: 338 HVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGE 397
            V +      L   +TVAENIAL      P             ++ ++L E+        
Sbjct: 87  MVFQ---HFSLFDTLTVAENIALGL----PRGSKTAAGSPHAGTNMKQLAEQIRETALRY 139

Query: 398 WVSAS------SLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARD 451
            +         +LS G +Q+  I R +   P LLI+ +PT  L   A++ +   L Q   
Sbjct: 140 GLPLEPNRHVHTLSVGERQRVEIVRALLAKPQLLILDEPTSVLTPQAVQTLFITLRQLAA 199

Query: 452 EGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGG 502
           EG ++L IS +LDEI  +     V+  G++ G+  P   +   L  LM+GG
Sbjct: 200 EGTSILYISHKLDEIRELCHSATVMRMGRVTGVCDPRQESAASLSRLMIGG 250


Lambda     K      H
   0.315    0.135    0.365 

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: 586
Number of extensions: 31
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: 506
Length of database: 529
Length adjustment: 35
Effective length of query: 471
Effective length of database: 494
Effective search space:   232674
Effective search space used:   232674
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 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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Protein sequences (fasta format)
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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