Alignments for a candidate for nupA in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Acidovorax sp. GW101-3H11

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 Ac3H11_2881 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= TCDB::A2RKA7
         (506 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2881
          Length = 496

 Score =  302 bits (774), Expect = 2e-86
 Identities = 179/495 (36%), Positives = 279/495 (56%), Gaps = 17/495 (3%)

Query: 7   IQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVK 66
           ++  +VTK FG       V   L+ G ++ LLGENGAGKSTLM IL+G   P+ GEV V 
Sbjct: 5   VEFRNVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVD 64

Query: 67  GKLENIDSPSKAANL-GIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILE 125
           G +      S+AA   GI ++HQ F L D  T+ +NI LG+E+ +G+ LD K  ++K  E
Sbjct: 65  GAVRAPGGGSRAAEAQGIVLIHQEFNLADDLTIAQNIFLGHEIKRGLFLDDKAMREKTRE 124

Query: 126 LSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIM 185
              + GL ++PD  +R + V ++Q VEI + L R A +LI DEPTA LTP E   L  +M
Sbjct: 125 ALAKVGLPLDPDTRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETERLFALM 184

Query: 186 KNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSF 245
             L   G +II I+HKLDE+    D + V+R G  +        T +++A LMVGR ++ 
Sbjct: 185 AGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLMVGRELAD 244

Query: 246 ITEKAAAQPKD--VVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVK 303
           +       P+D    + ++ L +         +G+  +VR GEI+G AG+ G G+TEL +
Sbjct: 245 LFPPKLPAPQDGAPAITVRGLTVPG-----WAEGVDFEVRRGEILGFAGLVGAGRTELFE 299

Query: 304 AITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENI---AL 360
            + GL    +G++++  + +  + PR      + ++ EDR   GL +   +  N+   AL
Sbjct: 300 GLLGLRPRTAGTVEIAGQPVQLKSPRDAARHGLTYLSEDRKGKGLHVHFGLRPNLTLMAL 359

Query: 361 QTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDR 420
           + Y KP      +LD     +  RE ++EF +R     V ASSLSGGNQQK  +A+ +  
Sbjct: 360 ERYAKP------WLDPAAEQAALREAVQEFGIRTGSLEVRASSLSGGNQQKLALAKVLHP 413

Query: 421 NPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQ 480
            P ++++ +PTRG+DVGA   I+  + +  ++G AV+VIS EL E++ +  R+AV+  G+
Sbjct: 414 GPSVVVLDEPTRGVDVGAKREIYHLVQRLAEQGLAVIVISSELMELIGLCHRVAVMRAGR 473

Query: 481 IQGIVSPETTTKQEL 495
           +Q  +     T++EL
Sbjct: 474 LQTTLQEPHLTEEEL 488



 Score = 68.9 bits (167), Expect = 4e-16
 Identities = 57/239 (23%), Positives = 110/239 (46%), Gaps = 10/239 (4%)

Query: 265 NIKESRGSLKV-KGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNK-D 322
           N+ +  G ++V  G+   ++ G + G+ G +G G++ L+K + G     +G + +     
Sbjct: 9   NVTKEFGPVRVLHGVGFALQPGRVYGLLGENGAGKSTLMKILAGYESPTTGEVVVDGAVR 68

Query: 323 ITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINSH 382
                 R    Q +  + ++ +   L  ++T+A+NI L    K  +    FLD   +   
Sbjct: 69  APGGGSRAAEAQGIVLIHQEFN---LADDLTIAQNIFLGHEIKRGL----FLDDKAMREK 121

Query: 383 ARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYI 442
            RE + +  +    +      L    +Q   IAR + RN  LLI+ +PT  L  G  E +
Sbjct: 122 TREALAKVGLPLDPD-TRVRKLIVAEKQLVEIARALARNARLLIMDEPTATLTPGETERL 180

Query: 443 HKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVG 501
              +   +  G  ++ IS +LDE+   +D + V+ DG +    +  + T++++  LMVG
Sbjct: 181 FALMAGLKAAGVTIIYISHKLDEVERTTDEVVVMRDGLLVAREATASVTRRQMANLMVG 239


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: 561
Number of extensions: 35
Number of successful extensions: 7
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: 496
Length adjustment: 34
Effective length of query: 472
Effective length of database: 462
Effective search space:   218064
Effective search space used:   218064
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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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