Alignments for a candidate for nupA in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_4286 Inositol transport system ATP-binding protein

Query= TCDB::A2RKA7
         (506 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4286
          Length = 526

 Score =  309 bits (792), Expect = 1e-88
 Identities = 172/497 (34%), Positives = 286/497 (57%), Gaps = 8/497 (1%)

Query: 6   VIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHV 65
           ++++I+V+K F   VA   V L ++ G + AL+GENGAGKSTLM I++G+ +P  GE+ +
Sbjct: 32  LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 91

Query: 66  KGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINL-DLKTAKKKIL 124
           +GK    ++P  A   GI M+HQ   L+   ++ ENI +G E   G+++ D +   +   
Sbjct: 92  RGKPVVFETPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMIDHREMHRCTA 151

Query: 125 ELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQI 184
           +L ER  ++++P+ L+ ++S+ ++Q VEI K +   +DILI DEPT+ +T  E+  L  I
Sbjct: 152 KLLERLRINLDPEELVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 211

Query: 185 MKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVS 244
           + +L ++GK II ITHK++E+ ++AD + V R G  I            L  +MVGR +S
Sbjct: 212 IADLKRQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 271

Query: 245 FITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKA 304
            +         D++L ++DL +         K +S D+ AGEI+G+AG+ G+G+T + +A
Sbjct: 272 QLFPVREKPIGDLLLSVRDLKLDGI-----FKDVSFDLHAGEILGIAGLMGSGRTNVAEA 326

Query: 305 ITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYY 364
           I G+T  D G I+L  + +    P    E+    + EDR   GL   ++V EN+ +    
Sbjct: 327 IFGITPSDGGEIRLDGEVVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVL- 385

Query: 365 KPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDL 424
            P     GF+    + +   ++ ++  V+         +LSGGNQQKA++AR +  NP +
Sbjct: 386 -PHYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRI 444

Query: 425 LIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGI 484
           LI+ +PTRG+DVGA   I++ +     EG AV++IS EL E+L +SDR+ V+H+G + G 
Sbjct: 445 LILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGT 504

Query: 485 VSPETTTKQELGILMVG 501
           +     T++ +  L  G
Sbjct: 505 LDRSEATQERVMQLASG 521



 Score = 90.9 bits (224), Expect = 1e-22
 Identities = 55/256 (21%), Positives = 132/256 (51%), Gaps = 8/256 (3%)

Query: 252 AQPKDVVLEIKDLNIKES-RGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTK 310
           A P D    ++ +N+ +   G + +  + L VR G ++ + G +G G++ L+K I G+ +
Sbjct: 24  ATPVDEPYLLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQ 83

Query: 311 VDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSK 370
            D+G ++L  K +  + P    +  +  + ++ +   L+  M++AENI +    +  ++ 
Sbjct: 84  PDAGELRLRGKPVVFETPLAALQAGIAMIHQELN---LMPHMSIAENIWIG---REQLNG 137

Query: 371 YGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQP 430
              +D+ +++    +L+E   +    E +   +LS   +Q   IA+ +  + D+LI+ +P
Sbjct: 138 LHMIDHREMHRCTAKLLERLRINLDPEEL-VGNLSIAERQMVEIAKAVSYDSDILIMDEP 196

Query: 431 TRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETT 490
           T  +    + ++   +   + +GK ++ I+ +++E+ +++D +AV  DG   G+   ++ 
Sbjct: 197 TSAITDKEVAHLFSIIADLKRQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSM 256

Query: 491 TKQELGILMVGGNINE 506
               L  +MVG  +++
Sbjct: 257 DGDSLISMMVGRELSQ 272



 Score = 80.5 bits (197), Expect = 1e-19
 Identities = 55/225 (24%), Positives = 109/225 (48%), Gaps = 8/225 (3%)

Query: 25  VNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVKGKLENIDSPSKAANLGIG 84
           V+ +L  GEI  + G  G+G++ +   + G+     GE+ + G++  I  P  A   G  
Sbjct: 300 VSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEIRLDGEVVRISDPHMAIEKGFA 359

Query: 85  MVHQHFMLVDAF---TVTENI---ILGNEVTKGINLDLKTAKKKILELSERYGLSVEP-D 137
           ++ +   L   F   +V EN+   +L + V  G  +  K  +    ++ ++  +     +
Sbjct: 360 LLTEDRKLSGLFPCLSVLENMEMAVLPHYVGNGF-IQQKALRALCEDMCKKLRVKTPSLE 418

Query: 138 ALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLIKEGKSIIL 197
             I  +S G QQ+  + + L     ILI DEPT  +      E+ +++  L  EG ++I+
Sbjct: 419 QCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIM 478

Query: 198 ITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRS 242
           I+ +L E+  ++DR+ V+  G  + T++  + T + + +L  G S
Sbjct: 479 ISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGMS 523


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: 596
Number of extensions: 27
Number of successful extensions: 7
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: 526
Length adjustment: 35
Effective length of query: 471
Effective length of database: 491
Effective search space:   231261
Effective search space used:   231261
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.

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 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