Alignments for a candidate for nupA in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Pseudomonas fluorescens FW300-N2C3

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 AO356_23205 AO356_23205 D-ribose transporter ATP-binding protein

Query= TCDB::A2RKA7
         (506 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_23205
          Length = 517

 Score =  308 bits (789), Expect = 3e-88
 Identities = 172/497 (34%), Positives = 282/497 (56%), Gaps = 8/497 (1%)

Query: 6   VIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHV 65
           ++++++V+K F   VA   V L ++ G + AL+GENGAGKSTLM I++G+ +P  GE+ +
Sbjct: 26  LLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 85

Query: 66  KGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINL-DLKTAKKKIL 124
           +GK    D+P  A   GI M+HQ   L+   ++ ENI +G E   G+++ D     +   
Sbjct: 86  RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMVDHGEMHRCTA 145

Query: 125 ELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQI 184
            L ER  + ++P+  + ++S+ ++Q VEI K +   +DILI DEPT+ +T  E+  L  I
Sbjct: 146 RLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLFSI 205

Query: 185 MKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVS 244
           + +L  +GK II ITHK++E+ A+AD + V R G  I            L  +MVGR +S
Sbjct: 206 IADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 265

Query: 245 FITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKA 304
            +         ++VL ++DL++         KG+S D+ AGEI+G+AG+ G+G+T + +A
Sbjct: 266 QLFPVREQPIGELVLSVRDLSLDGI-----FKGVSFDLHAGEILGIAGLMGSGRTNVAEA 320

Query: 305 ITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYY 364
           I G+T    G I+L  + +    P    E+    + EDR   GL   ++V EN+ +    
Sbjct: 321 IFGVTPSTGGEIRLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVL- 379

Query: 365 KPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDL 424
            P     GF+    + +   ++ ++  V+         +LSGGNQQKA++AR +  NP +
Sbjct: 380 -PHYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRI 438

Query: 425 LIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGI 484
           LI+ +PTRG+DVGA   I++ +     EG AV++IS EL E+L +SDR+ V+H+G + G 
Sbjct: 439 LILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGT 498

Query: 485 VSPETTTKQELGILMVG 501
           +     T++ +  L  G
Sbjct: 499 LDRSEATQERVMQLASG 515



 Score = 90.9 bits (224), Expect = 1e-22
 Identities = 55/249 (22%), Positives = 129/249 (51%), Gaps = 8/249 (3%)

Query: 258 VLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIK 317
           +LE+ +++ K   G + +  + L VR G ++ + G +G G++ L+K I G+ + D+G ++
Sbjct: 26  LLEVVNVS-KGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELR 84

Query: 318 LHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYN 377
           L  K +T   P    +  +  + ++ +   L+  M++AENI +    +  ++    +D+ 
Sbjct: 85  LRGKPVTFDTPLAALQAGIAMIHQELN---LMPHMSIAENIWIG---REQLNGLHMVDHG 138

Query: 378 KINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVG 437
           +++     L+E   ++   E     +LS   +Q   IA+ +  + D+LI+ +PT  +   
Sbjct: 139 EMHRCTARLLERLRIKLDPE-EQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITET 197

Query: 438 AIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGI 497
            + ++   +   + +GK ++ I+ +++E+  ++D +AV  DG   G+   ++     L  
Sbjct: 198 EVAHLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLIS 257

Query: 498 LMVGGNINE 506
           +MVG  +++
Sbjct: 258 MMVGRELSQ 266



 Score = 78.6 bits (192), Expect = 5e-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: 294 VSFDLHAGEILGIAGLMGSGRTNVAEAIFGVTPSTGGEIRLDGQPVRISDPHMAIEKGFA 353

Query: 85  MVHQHFMLVDAF---TVTENI---ILGNEVTKGINLDLKTAKKKILELSERYGLSVEP-D 137
           ++ +   L   F   +V EN+   +L + V  G  +  K  +    ++ ++  +     +
Sbjct: 354 LLTEDRKLSGLFPCLSVLENMEMAVLPHYVGNGF-IQQKALRALCEDMCKKLRVKTPSLE 412

Query: 138 ALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLIKEGKSIIL 197
             I  +S G QQ+  + + L     ILI DEPT  +      E+ +++  L  EG ++I+
Sbjct: 413 QCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIM 472

Query: 198 ITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRS 242
           I+ +L E+  ++DR+ V+  G  + T++  + T + + +L  G S
Sbjct: 473 ISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASGLS 517


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: 580
Number of extensions: 19
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: 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
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