Alignments for a candidate for nupA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Phaeobacter inhibens BS107

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 GFF2274 PGA1_c23060 ribose import ATP-binding protein RbsA

Query= TCDB::A2RKA7
         (506 letters)



>FitnessBrowser__Phaeo:GFF2274
          Length = 503

 Score =  285 bits (728), Expect = 3e-81
 Identities = 173/491 (35%), Positives = 269/491 (54%), Gaps = 8/491 (1%)

Query: 6   VIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHV 65
           V+++  + K F    A D V+L +  GE+HAL+GENGAGKSTLM +L G+ +P EG++ V
Sbjct: 7   VLRLEGIVKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQIIV 66

Query: 66  KGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINL-DLKTAKKKIL 124
             +   +  P  A   GI  +HQ   L D  +V ENI LG    K   L D    + K  
Sbjct: 67  AEQPVVMSGPLDAKAKGIVFIHQELSLADELSVAENIYLGELPRKRFGLVDWAELEAKTN 126

Query: 125 ELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQI 184
            + E+  +       + D+S+  QQ VEI + L   A  +IFDEPTA LT AE   L ++
Sbjct: 127 AILEKLKVGFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVLFEV 186

Query: 185 MKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVS 244
           + +L ++G  I  I+H+++EI  + DRI+V+R G+   TV   +   + + ++M+GR + 
Sbjct: 187 ISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIGRKLD 246

Query: 245 FITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKA 304
               +A  +  +V LE++ L    S GSL  + ++ +VR GE+VG  G+ G G+TE+ + 
Sbjct: 247 LSRNEAHHELGEVALEVRGL----SCGSL-FEDVNFEVRRGEVVGFYGLVGAGRTEIAET 301

Query: 305 ITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYY 364
           + GL    SGSI L   ++    P    E+ +  VPEDR   GLVL M   +N+ L    
Sbjct: 302 LFGLRNPTSGSIFLDGAEVAITSPHDAIERGISLVPEDRKGQGLVLGMNCRDNMTLPQV- 360

Query: 365 KPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDL 424
              +    F+      +   +  ++ D+R  G      +LSGGNQQK +I + +   P++
Sbjct: 361 -DDLKAGPFVADGAEIAIFDQYRDKLDIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNV 419

Query: 425 LIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGI 484
           LIV +PTRG+DVG+   IH  L     +G AV+VIS E+ E+L+V+DRI  ++ G+I   
Sbjct: 420 LIVDEPTRGIDVGSKAEIHNLLRDLAAQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRT 479

Query: 485 VSPETTTKQEL 495
            + E  T++ L
Sbjct: 480 FTSEEVTEENL 490



 Score = 96.3 bits (238), Expect = 2e-24
 Identities = 61/240 (25%), Positives = 119/240 (49%), Gaps = 7/240 (2%)

Query: 266 IKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITN 325
           +K   G   + G+SL +  GE+  + G +G G++ L+K + G+ + D G I +  + +  
Sbjct: 14  VKTFPGVRALDGVSLTILPGEVHALMGENGAGKSTLMKVLGGIHQPDEGQIIVAEQPVVM 73

Query: 326 QRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINSHARE 385
             P     + +  + ++     L  E++VAENI L      P  ++G +D+ ++ +    
Sbjct: 74  SGPLDAKAKGIVFIHQEL---SLADELSVAENIYLGEL---PRKRFGLVDWAELEAKTNA 127

Query: 386 LMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKR 445
           ++E+  V G         LS  NQQ   IAR +  +   +I  +PT  L       + + 
Sbjct: 128 ILEKLKV-GFNAKTRVGDLSIANQQMVEIARALTVDAKAVIFDEPTASLTDAEKVVLFEV 186

Query: 446 LIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGGNIN 505
           +   +++G  +  IS  ++EI  ++DRI+V+ DGQ QG V+   T ++ +  +M+G  ++
Sbjct: 187 ISDLQEQGVGIAYISHRMEEIFKITDRISVLRDGQYQGTVNTAETNEENVTQMMIGRKLD 246



 Score = 80.9 bits (198), Expect = 1e-19
 Identities = 64/242 (26%), Positives = 114/242 (47%), Gaps = 24/242 (9%)

Query: 23  DKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVKGKLENIDSPSKAANLG 82
           + VN E+++GE+    G  GAG++ +   L GL  P+ G + + G    I SP  A   G
Sbjct: 273 EDVNFEVRRGEVVGFYGLVGAGRTEIAETLFGLRNPTSGSIFLDGAEVAITSPHDAIERG 332

Query: 83  IGMVHQHFMLVDAFTVTENIILGNEVTKGINL----DLKT----AKKKILELSERYGLSV 134
           I +V +           + ++LG      + L    DLK     A    + + ++Y   +
Sbjct: 333 ISLVPED-------RKGQGLVLGMNCRDNMTLPQVDDLKAGPFVADGAEIAIFDQYRDKL 385

Query: 135 EPDA-----LIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLI 189
           +        L+ ++S G QQ++ I K L    ++LI DEPT  +      E+  ++++L 
Sbjct: 386 DIRTPGWKQLVGNLSGGNQQKIVIGKWLSMRPNVLIVDEPTRGIDVGSKAEIHNLLRDLA 445

Query: 190 KEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSVSFITEK 249
            +G ++I+I+ ++ E+  VADRI  +  G+ + T    + T + L   + G      TEK
Sbjct: 446 AQGYAVIVISSEMPEVLHVADRIVAMYSGRIMRTFTSEEVTEENLIAAISGLD----TEK 501

Query: 250 AA 251
            A
Sbjct: 502 VA 503


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: 636
Number of extensions: 33
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: 503
Length adjustment: 34
Effective length of query: 472
Effective length of database: 469
Effective search space:   221368
Effective search space used:   221368
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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