Alignments for a candidate for nupA in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Sinorhizobium meliloti 1021

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 SM_b20124 SM_b20124 sugar ABC transporter ATP-binding protein

Query= TCDB::A2RKA7
         (506 letters)



>FitnessBrowser__Smeli:SM_b20124
          Length = 508

 Score =  459 bits (1182), Expect = e-134
 Identities = 228/501 (45%), Positives = 336/501 (67%)

Query: 1   MANETVIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSE 60
           MA + ++ M  + KRFG  + +  V L++++ EIHALLGENGAGK+ LM+IL G+L P+E
Sbjct: 1   MAGKQLLLMDGIHKRFGPLIVSAGVTLDVEENEIHALLGENGAGKTVLMSILCGVLSPNE 60

Query: 61  GEVHVKGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTKGINLDLKTAK 120
           G++  KG+   + SP +A    IGMVHQHFMLV   TV EN +LG      +  D++   
Sbjct: 61  GQIVFKGRPLKLGSPREAIKHRIGMVHQHFMLVPNLTVAENYVLGQGSPFSMIRDMRAVH 120

Query: 121 KKILELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITE 180
            +ILELS+RYGL V PDAL+  +SVG++QRVEILK LY G ++LI DEPTAVLTP E   
Sbjct: 121 ARILELSDRYGLDVAPDALVSSLSVGERQRVEILKVLYHGIELLILDEPTAVLTPQETDR 180

Query: 181 LMQIMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVG 240
           L+ +++ L+ +GK++I I+HKLDE+  V+DR++V+R  K + TV+  + T +ELA +MVG
Sbjct: 181 LLHLLRQLVADGKTVIFISHKLDEVMRVSDRVSVMRDAKVVRTVKTSETTARELARMMVG 240

Query: 241 RSVSFITEKAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTE 300
           R V     +A  +P  VVL ++ L+     G   ++ +S +VRA EIVG+AG+ GNGQ+E
Sbjct: 241 RDVLMYLPRAPLEPGRVVLSVEHLSCDGEAGLPALRDVSFEVRANEIVGIAGVSGNGQSE 300

Query: 301 LVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIAL 360
           L  A+TGL  V SGS+ L    +      +I +  + H+PEDRHR G+VL + + EN+ L
Sbjct: 301 LALALTGLLPVASGSVTLDGTQLAGLSSYEINQLPMAHIPEDRHRMGIVLPLPLTENVIL 360

Query: 361 QTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDR 420
           Q + KPP S  G LD N+I    R+LM  F V+ +G      +LSGGNQQK ++ RE+DR
Sbjct: 361 QRFDKPPFSSRGLLDLNEITRQTRDLMRRFKVKASGPGDRIRNLSGGNQQKLVVGRELDR 420

Query: 421 NPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQ 480
             D L+++Q TRG+D+GA E +  ++++ R  GKA+L+IS EL+E+  +SDRI V+++G+
Sbjct: 421 RFDFLLINQLTRGIDIGATELVMHKILEQRSAGKAILLISTELEELFTLSDRILVMYEGR 480

Query: 481 IQGIVSPETTTKQELGILMVG 501
           + G + P+ +  +E+G+LM G
Sbjct: 481 LVGEIPPDRSRLEEIGLLMAG 501



 Score = 93.6 bits (231), Expect = 2e-23
 Identities = 68/228 (29%), Positives = 116/228 (50%), Gaps = 8/228 (3%)

Query: 277 GLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITNQRPRKITEQSV 336
           G++LDV   EI  + G +G G+T L+  + G+   + G I    + +    PR+  +  +
Sbjct: 24  GVTLDVEENEIHALLGENGAGKTVLMSILCGVLSPNEGQIVFKGRPLKLGSPREAIKHRI 83

Query: 337 GHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYGFLDYNKINSHARELMEEFDVRGAG 396
           G V +      LV  +TVAEN  L       M +    D   +++   EL + + +  A 
Sbjct: 84  GMVHQHFM---LVPNLTVAENYVLGQGSPFSMIR----DMRAVHARILELSDRYGLDVAP 136

Query: 397 EWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAV 456
           + +  SSLS G +Q+  I + +    +LLI+ +PT  L     + +   L Q   +GK V
Sbjct: 137 DAL-VSSLSVGERQRVEILKVLYHGIELLILDEPTAVLTPQETDRLLHLLRQLVADGKTV 195

Query: 457 LVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVGGNI 504
           + IS +LDE++ VSDR++V+ D ++   V    TT +EL  +MVG ++
Sbjct: 196 IFISHKLDEVMRVSDRVSVMRDAKVVRTVKTSETTARELARMMVGRDV 243



 Score = 70.9 bits (172), Expect = 1e-16
 Identities = 63/229 (27%), Positives = 113/229 (49%), Gaps = 14/229 (6%)

Query: 25  VNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVKGKLENIDSPSKAANLGIG 84
           V+ E++  EI  + G +G G+S L   L+GLL  + G V + G    +   S      + 
Sbjct: 278 VSFEVRANEIVGIAGVSGNGQSELALALTGLLPVASGSVTLDGT--QLAGLSSYEINQLP 335

Query: 85  MVH----QHFM-LVDAFTVTENIILGNE-----VTKGINLDLKTAKKKILELSERYGLSV 134
           M H    +H M +V    +TEN+IL         ++G+ LDL    ++  +L  R+ +  
Sbjct: 336 MAHIPEDRHRMGIVLPLPLTENVILQRFDKPPFSSRGL-LDLNEITRQTRDLMRRFKVKA 394

Query: 135 E-PDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLIKEGK 193
             P   IR++S G QQ++ + + L R  D L+ ++ T  +       +M  +      GK
Sbjct: 395 SGPGDRIRNLSGGNQQKLVVGRELDRRFDFLLINQLTRGIDIGATELVMHKILEQRSAGK 454

Query: 194 SIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRS 242
           +I+LI+ +L+E+  ++DRI V+  G+ +  +       +E+  LM G+S
Sbjct: 455 AILLISTELEELFTLSDRILVMYEGRLVGEIPPDRSRLEEIGLLMAGKS 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: 712
Number of extensions: 37
Number of successful extensions: 5
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: 508
Length adjustment: 34
Effective length of query: 472
Effective length of database: 474
Effective search space:   223728
Effective search space used:   223728
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