Alignments for a candidate for nupA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for nupA in Herbaspirillum seropedicae SmR1

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 HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein

Query= TCDB::A2RKA7
         (506 letters)



>FitnessBrowser__HerbieS:HSERO_RS05250
          Length = 520

 Score =  318 bits (815), Expect = 3e-91
 Identities = 184/493 (37%), Positives = 291/493 (59%), Gaps = 10/493 (2%)

Query: 6   VIQMIDVTKRFGDFVANDKVNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHV 65
           VI + +V KRF   +A D    EL  GE+HAL+GENGAGKSTLM ILSG+ +   G++ +
Sbjct: 22  VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81

Query: 66  KGKLENIDSPSKAANLGIGMVHQHFMLVDAFTVTENIILGNEVTK--GINLDLKTAKKKI 123
            GK   I  P +A  LGIG++HQ   L++  +  +NI +G E  K  G+ +D     ++ 
Sbjct: 82  DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141

Query: 124 LELSERYGLSVEPDALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQ 183
             +  R  L ++P   + +++V +QQ VEI K L   + +LI DEPTA L  AEI EL +
Sbjct: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201

Query: 184 IMKNLIKEGKSIILITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGRSV 243
           I+++L  +G  I+ I+HK+DE+R +ADR++V+R GK I TV + + +   +  +MVGR++
Sbjct: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261

Query: 244 SFITE-KAAAQPKDVVLEIKDLNIKESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELV 302
                        DVVLE++ LN    RG   ++ +S  +R GEI+G AG+ G G+TE+ 
Sbjct: 262 DGEQRIPPDTSRNDVVLEVRGLN----RGR-AIRDVSFTLRKGEILGFAGLMGAGRTEVA 316

Query: 303 KAITGLTKVDSGSIKLHNKDITNQRPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQT 362
           +AI G   +++G I +H      + P       +G++ EDR   GL + M V  NIAL +
Sbjct: 317 RAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSS 376

Query: 363 YYKPPMSKYGFLDYNKINSHARELMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNP 422
             +   ++ GF+D   I   A+  + +  ++       A  LSGGNQQK +IA+ + R+ 
Sbjct: 377 MGR--FTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDC 434

Query: 423 DLLIVSQPTRGLDVGAIEYIHKRLIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQ 482
           D+L   +PTRG+DVGA   I+K L    ++GKA+++IS EL E+L +S R+ V+ +G+I 
Sbjct: 435 DILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRIT 494

Query: 483 GIVSPETTTKQEL 495
           G ++    T++++
Sbjct: 495 GELARADATQEKI 507



 Score = 89.7 bits (221), Expect = 2e-22
 Identities = 66/225 (29%), Positives = 112/225 (49%), Gaps = 10/225 (4%)

Query: 25  VNLELKKGEIHALLGENGAGKSTLMNILSGLLEPSEGEVHVKGKLENIDSPSKAANLGIG 84
           V+  L+KGEI    G  GAG++ +   + G      GE+ + G    I SP+ A   GIG
Sbjct: 292 VSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIG 351

Query: 85  MVHQ---HFMLVDAFTVTENIILGN--EVTKGINLDLKTAKKKILELSERYGL---SVEP 136
            + +   HF L     V  NI L +    T+   +D +  ++       +  +   SVE 
Sbjct: 352 YLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQ 411

Query: 137 DALIRDISVGQQQRVEILKTLYRGADILIFDEPTAVLTPAEITELMQIMKNLIKEGKSII 196
            A  R +S G QQ++ I K L R  DIL FDEPT  +     +E+ +++  L ++GK+I+
Sbjct: 412 QA--RLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIV 469

Query: 197 LITHKLDEIRAVADRITVIRRGKSIDTVELGDKTNQELAELMVGR 241
           +I+ +L E+  ++ R+ V+  G+    +   D T +++ +L   R
Sbjct: 470 MISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLATQR 514



 Score = 83.6 bits (205), Expect = 2e-20
 Identities = 57/236 (24%), Positives = 117/236 (49%), Gaps = 8/236 (3%)

Query: 267 KESRGSLKVKGLSLDVRAGEIVGVAGIDGNGQTELVKAITGLTKVDSGSIKLHNKDITNQ 326
           K   G L +     ++ AGE+  + G +G G++ L+K ++G+ + DSG I L  K +   
Sbjct: 30  KRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEIT 89

Query: 327 RPRKITEQSVGHVPEDRHRDGLVLEMTVAENIALQTYYKPPMSKYG-FLDYNKINSHARE 385
            PR+     +G + ++ +   L+  ++ A+NI +    + P    G F+D +++N  A  
Sbjct: 90  EPRQAQALGIGIIHQELN---LMNHLSAAQNIFIG---REPRKAMGLFIDEDELNRQAAA 143

Query: 386 LMEEFDVRGAGEWVSASSLSGGNQQKAIIAREIDRNPDLLIVSQPTRGLDVGAIEYIHKR 445
           +     +           L+   QQ   IA+ +  +  +LI+ +PT  L+   I  + + 
Sbjct: 144 IFARMRL-DMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRI 202

Query: 446 LIQARDEGKAVLVISFELDEILNVSDRIAVIHDGQIQGIVSPETTTKQELGILMVG 501
           +   + +G  ++ IS ++DE+  ++DR++V+ DG+    V  + T+   +  +MVG
Sbjct: 203 IRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258


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: 606
Number of extensions: 36
Number of successful extensions: 9
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: 520
Length adjustment: 35
Effective length of query: 471
Effective length of database: 485
Effective search space:   228435
Effective search space used:   228435
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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Candidates (tab-delimited)
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