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_2759 PP_2759 ribose ABC transporter - ATP-binding subunit

Query= TCDB::A2RKA7
         (506 letters)



>FitnessBrowser__Putida:PP_2759
          Length = 512

 Score =  286 bits (733), Expect = 9e-82
 Identities = 162/477 (33%), Positives = 271/477 (56%), Gaps = 8/477 (1%)

Query: 6   VIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHV 65
           V+++  + K FG   A D  +L +  G +H L+GENGAGKSTL+ +L+G+  P  G + +
Sbjct: 5   VLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSLLL 64

Query: 66  KGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILE 125
            G+     SP +   LGIG +HQ  +L   FTV E +  G+E   G  LD ++ +++   
Sbjct: 65  DGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHERRFGPLLDRRSQQREAAR 124

Query: 126 LSERY-GLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQI 184
           L + Y GL +  +ALI ++S  +QQ V+I++ L     +L+FDEP+  L   E+  L++I
Sbjct: 125 LLDDYFGLRLPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERLLRI 184

Query: 185 MKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVS 244
           ++ L  +G +I+ I+H L EI A+ DR+TV+R G+ +  V   + + +++  LMV R V 
Sbjct: 185 VQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQITRLMVNREVG 244

Query: 245 FITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKA 304
            +  K A     ++L+++ L    +      +G+ L VR GEIVG+ G+ G+G  EL+++
Sbjct: 245 ELYPKVAVPAGALLLDVRGLGRARA-----YQGIDLQVRRGEIVGLTGLVGSGAKELLRS 299

Query: 305 ITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYY 364
           + GL   DSG ++L  + ++ + PR+   Q V  +PE+R R G+ L+++V EN  L    
Sbjct: 300 LFGLAPPDSGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTLAALS 359

Query: 365 KPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDL 424
           +    + G L   +      EL+E   ++  G       LSGGNQQK  +A+   R   L
Sbjct: 360 R--FVRLGLLSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSSL 417

Query: 425 LIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQI 481
            ++ +P+ G+DVGA   I++ + +   EG  VL++S +L E++ + DRI V+H G I
Sbjct: 418 YLLDEPSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAI 474



 Score = 89.7 bits (221), Expect = 2e-22
 Identities = 65/240 (27%), Positives = 121/240 (50%), Gaps = 11/240 (4%)

Query: 9   MIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVKGK 68
           ++DV +  G   A   ++L++++GEI  L G  G+G   L+  L GL  P  GEV + G+
Sbjct: 258 LLDV-RGLGRARAYQGIDLQVRRGEIVGLTGLVGSGAKELLRSLFGLAPPDSGEVRLDGQ 316

Query: 69  LENIDSPSKAANLGIGMV----HQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKK-- 122
             ++ SP +A   G+ ++     +  + +D  +V EN  L   +++ + L L +  ++  
Sbjct: 317 PLSLRSPREAVAQGVALMPEERRRQGVALD-LSVQENTTLA-ALSRFVRLGLLSPARERH 374

Query: 123 -ILELSERYGLSVE-PDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITE 180
             LEL ER  +      A +R +S G QQ+V + K   R + + + DEP+  +      E
Sbjct: 375 TTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSSLYLLDEPSVGIDVGAKVE 434

Query: 181 LMQIMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVG 240
           + +++  L+KEG  +++++  L E+  + DRI V+ RG        G+  +  L  +  G
Sbjct: 435 IYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAARFAAGEANSDRLLAVATG 494



 Score = 89.0 bits (219), Expect = 4e-22
 Identities = 66/250 (26%), Positives = 122/250 (48%), Gaps = 10/250 (4%)

Query: 258 VLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIK 317
           VLE++ + +K    +  + G SL V AG + G+ G +G G++ L+K + G+ + D+GS+ 
Sbjct: 5   VLELRGI-VKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSLL 63

Query: 318 LHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYG-FLDY 376
           L  +   +  PR++    +G + ++R    L    TV E +     +     ++G  LD 
Sbjct: 64  LDGQPHGHFSPRQVERLGIGFIHQERL---LPARFTVGEAL-----FFGHERRFGPLLDR 115

Query: 377 NKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDV 436
                 A  L++++             LS   QQ   I R +   P +L+  +P+  L  
Sbjct: 116 RSQQREAARLLDDYFGLRLPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQ 175

Query: 437 GAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELG 496
             +E + + + + RD+G A++ IS  L EI  + DR+ V+ +G+    VSP  T+ +++ 
Sbjct: 176 REVERLLRIVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQIT 235

Query: 497 ILMVGGNINE 506
            LMV   + E
Sbjct: 236 RLMVNREVGE 245


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: 603
Number of extensions: 35
Number of successful extensions: 8
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: 512
Length adjustment: 34
Effective length of query: 472
Effective length of database: 478
Effective search space:   225616
Effective search space used:   225616
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