Alignments for a candidate for nupA in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Pseudomonas putida KT2440

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 PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit

Query= TCDB::A2RKA7
         (506 letters)



>FitnessBrowser__Putida:PP_2455
          Length = 524

 Score =  271 bits (694), Expect = 3e-77
 Identities = 171/484 (35%), Positives = 272/484 (56%), Gaps = 11/484 (2%)

Query: 1   MANETVIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSE 60
           +ANE V+    + K +   V  + V+L L+ GE+ AL GENGAGKSTL  ++SGL  P+ 
Sbjct: 11  LANEVVLAASGLGKTYAQPVLGE-VSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTT 69

Query: 61  GEVHVKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAK 120
           G +  +G+     S  +A  LG+ MV Q   L+   TV EN+ L N  ++   +  K  +
Sbjct: 70  GHMTYRGQAYAPGSRGEAERLGVRMVMQELNLLPTLTVAENLFLDNLPSRFGWISHKRLR 129

Query: 121 KKILELSERYGL-SVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEIT 179
           +       R GL +++PD  + ++ +G QQ VEI + L     +LI DEPTA+LT  E+ 
Sbjct: 130 QLATAAMARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVA 189

Query: 180 ELMQIMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMV 239
            L   ++ L   G +I+ I+H+L+E++ VA RI V+R GK +    +   ++ EL  LMV
Sbjct: 190 LLFTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLMV 249

Query: 240 GRSVSFITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQT 299
           GR +    +    Q    +L++  L     RG  KV+ +S +VRAGEI G++G+ G G+T
Sbjct: 250 GRELGEHIDLGRRQLGAPLLKVDKL----CRGD-KVREVSFEVRAGEIFGISGLIGAGRT 304

Query: 300 ELVKAITGLTKVDSGSIKLHN--KDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAEN 357
           EL++ I G  + DSG I L    + ++   P+      +  + EDR  +GL+L  +++ N
Sbjct: 305 ELLRLIYGADRADSGGIALGQPPQAVSIDSPKAAVRAGIALITEDRKGEGLLLTQSISAN 364

Query: 358 IALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIARE 417
           IAL       +S+ G LD     + A   ++   +R AG       LSGGNQQK +I R 
Sbjct: 365 IALGNL--GAVSRAGVLDSEAEKALAERQIQAMRIRSAGAQQVVGELSGGNQQKVVIGRW 422

Query: 418 IDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIH 477
           ++R+  +L+  +PTRG+DVGA   I+  L +   +GKA++V+S +L E++ + DRIAV+ 
Sbjct: 423 LERDCQVLLFDEPTRGIDVGAKFDIYGLLAELARQGKALVVVSSDLRELMLICDRIAVLS 482

Query: 478 DGQI 481
            G++
Sbjct: 483 AGRL 486



 Score = 84.3 bits (207), Expect = 9e-21
 Identities = 59/211 (27%), Positives = 112/211 (53%), Gaps = 14/211 (6%)

Query: 24  KVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHV--KGKLENIDSPSKAANL 81
           +V+ E++ GEI  + G  GAG++ L+ ++ G      G + +    +  +IDSP  A   
Sbjct: 282 EVSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIALGQPPQAVSIDSPKAAVRA 341

Query: 82  GIGMVHQHFM---LVDAFTVTENIILGN--EVTKGINLDLKT----AKKKILELSERYGL 132
           GI ++ +      L+   +++ NI LGN   V++   LD +     A+++I  +  R   
Sbjct: 342 GIALITEDRKGEGLLLTQSISANIALGNLGAVSRAGVLDSEAEKALAERQIQAMRIR--- 398

Query: 133 SVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLIKEG 192
           S     ++ ++S G QQ+V I + L R   +L+FDEPT  +      ++  ++  L ++G
Sbjct: 399 SAGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAELARQG 458

Query: 193 KSIILITHKLDEIRAVADRITVIRRGKSIDT 223
           K++++++  L E+  + DRI V+  G+ IDT
Sbjct: 459 KALVVVSSDLRELMLICDRIAVLSAGRLIDT 489



 Score = 79.7 bits (195), Expect = 2e-19
 Identities = 60/229 (26%), Positives = 109/229 (47%), Gaps = 7/229 (3%)

Query: 278 LSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVG 337
           +SL +RAGE++ + G +G G++ L K I+GL    +G +    +        +     V 
Sbjct: 34  VSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTYRGQAYAPGSRGEAERLGVR 93

Query: 338 HVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGE 397
            V ++ +   L+  +TVAEN+ L        S++G++ + ++   A   M    +     
Sbjct: 94  MVMQELN---LLPTLTVAENLFLDNL----PSRFGWISHKRLRQLATAAMARVGLDAIDP 146

Query: 398 WVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVL 457
                 L  G+QQ   IAR +  +  +LI+ +PT  L    +  +  ++ + R  G A++
Sbjct: 147 DTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALLFTQIERLRARGVAIV 206

Query: 458 VISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGGNINE 506
            IS  L+E+  V+ RI V+ DG++      +  +  EL  LMVG  + E
Sbjct: 207 YISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSSAELVNLMVGRELGE 255


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: 633
Number of extensions: 41
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: 506
Length of database: 524
Length adjustment: 35
Effective length of query: 471
Effective length of database: 489
Effective search space:   230319
Effective search space used:   230319
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