Alignments for a candidate for nupA in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_3911 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= TCDB::A2RKA7
         (506 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3911
          Length = 517

 Score =  283 bits (723), Expect = 1e-80
 Identities = 172/474 (36%), Positives = 272/474 (57%), Gaps = 10/474 (2%)

Query: 25  VNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVKGKLENIDSPSKAANLGIG 84
           ++L L +GE+ AL GENGAGKSTL  I+ GL+ P+ G++  +G+     S ++A  LGI 
Sbjct: 27  IDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQYQGQDYRPGSRAQAEALGIR 86

Query: 85  MVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAKKKILELSERYGL-SVEPDALIRDI 143
           MV Q   L+   +V EN+ L N  +KG  +  K  +K  +E     GL +++PD L+ ++
Sbjct: 87  MVMQELNLLPTLSVAENLFLDNLPSKGGWISRKQLRKAAIEAMAHVGLDAIDPDTLVGEL 146

Query: 144 SVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLIKEGKSIILITHKLD 203
            +G QQ VEI + L     +LI DEPTA+LT  E+  L + +  L   G SII I+H+L+
Sbjct: 147 GIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQSRGVSIIYISHRLE 206

Query: 204 EIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSFITEKAAAQPKDVVLEIKD 263
           E+  VA RI V+R G  +    + +  +++L  LMVGR +    +  A +    VL +  
Sbjct: 207 ELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLMVGRELGEHIDMGARKIGAPVLTVNG 266

Query: 264 LNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKL--HNK 321
           L+  +     KV+ +S +VRAGEI G++G+ G G+TEL++ I G    DSG+I L    +
Sbjct: 267 LSRSD-----KVRDVSFEVRAGEIFGISGLIGAGRTELLRLIFGADIADSGTIALGAPAQ 321

Query: 322 DITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINS 381
            I  + P       +  + EDR  +GL+L  ++  NIAL     P +S  GF+D +K  +
Sbjct: 322 VINVRSPVDAVGHGIALITEDRKGEGLLLTQSIGANIALGN--MPGISGAGFVDNDKERA 379

Query: 382 HARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEY 441
            A+  ++   +R +G     S LSGGNQQK +I R ++R+  +L+  +PTRG+DVGA   
Sbjct: 380 LAQRQIDAMRIRSSGPAQLVSELSGGNQQKVVIGRWLERDCSVLLFDEPTRGIDVGAKFD 439

Query: 442 IHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQEL 495
           I+  L +   +GKA++V+S +L E++ + DRI V+  G +      ++ T+ EL
Sbjct: 440 IYNLLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGSLIDTFDRDSWTQDEL 493



 Score = 83.2 bits (204), Expect = 2e-20
 Identities = 59/230 (25%), Positives = 107/230 (46%), Gaps = 7/230 (3%)

Query: 277 GLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSV 336
           G+ L +  GE++ + G +G G++ L K I GL    +G ++   +D    RP    +   
Sbjct: 26  GIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQYQGQDY---RPGSRAQAEA 82

Query: 337 GHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAG 396
             +        L+  ++VAEN+ L        SK G++   ++   A E M    +    
Sbjct: 83  LGIRMVMQELNLLPTLSVAENLFLDNL----PSKGGWISRKQLRKAAIEAMAHVGLDAID 138

Query: 397 EWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAV 456
                  L  G+QQ   IAR +  +  +LI+ +PT  L    +E + +++ + +  G ++
Sbjct: 139 PDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQSRGVSI 198

Query: 457 LVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGGNINE 506
           + IS  L+E+  V+ RIAV+ DG +  +        ++L  LMVG  + E
Sbjct: 199 IYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLMVGRELGE 248


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: 650
Number of extensions: 38
Number of successful extensions: 8
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: 517
Length adjustment: 35
Effective length of query: 471
Effective length of database: 482
Effective search space:   227022
Effective search space used:   227022
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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 2024 update 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