GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcA in Cupriavidus basilensis 4G11

Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate RR42_RS30800 RR42_RS30800 sugar ABC transporter ATP-binding protein

Query= uniprot:A0A0C4Y5F6
         (540 letters)



>FitnessBrowser__Cup4G11:RR42_RS30800
          Length = 530

 Score =  263 bits (672), Expect = 1e-74
 Identities = 179/520 (34%), Positives = 271/520 (52%), Gaps = 53/520 (10%)

Query: 12  PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71
           P+L L  I K F  + A   + L    GEV AL+GENGAGKSTL+ IL G Y AD  G  
Sbjct: 4   PILRLAGITKRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVAD-AGTV 62

Query: 72  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRA----LQRRGLVARGDM 127
            +DGQ +    P++A   G+ +++Q  +LA NLSV +NI LG       +  G  ARG +
Sbjct: 63  EVDGQPLPPGQPRAALTAGIGMVHQHFTLADNLSVLDNIMLGTQPLWQWRLDGHAARGKV 122

Query: 128 VRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETD 187
           +        R G    P A V  LS+ +RQ VEI +A++  AR+L++DEPT  L+ HE +
Sbjct: 123 LALAE----RFGLAVRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAE 178

Query: 188 RLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMV 247
            LF+ + QL  EG+++++ISH++ E+  ++DR+ VLR G  V     A  ++A L ++MV
Sbjct: 179 TLFSTLAQLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMV 238

Query: 248 GRDLSGFYTKTHGQAVEREVMLSVRDVADGRR--------------------VKGCSFDL 287
           GR ++           ER    S  D A+G                      ++  S  +
Sbjct: 239 GRVVA---------MPERVARRSAEDGANGNAAPPVLALEHVGARAANGRALLREVSLQV 289

Query: 288 RAGEVLGLAGLVGAGRTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAG 347
           RAGE++G+AG+ G G+  LA L  G    + G + +A    S          PR  I AG
Sbjct: 290 RAGEIVGIAGVSGNGQAALAELASGMLEASEGRITLAGKPMS--------AKPRAWIGAG 341

Query: 348 IAYLTEDRKLQGLFLDQSVHEN-INLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVA 406
           +A + EDR   G+  D +V EN ++  ++       G + R AA+R   + +    +R A
Sbjct: 342 VARVPEDRHAIGVVGDLAVWENAVSEQLSEPRFSRWGVIRRAAAQRFARDLVARFDVRTA 401

Query: 407 HAQVNVGALSGGNQQKVMLSRLLEIQ-----PRVLILDEPTRGVDIGAKSEIYRLINALA 461
              V    +SGGN QK++L R L ++     PR+++  +PT G+DIGA + +   +   A
Sbjct: 402 GIDVPARTMSGGNMQKLILGRALSVRGEGSAPRLVVASQPTWGLDIGAVAYVRARLLDAA 461

Query: 462 QSGVAILMISSELPEVVGLCDRVLVMREGTLAGEVRPAGS 501
           + G A+L+IS +L E+  L DR+ VM  G L  E RP  +
Sbjct: 462 REGAAVLLISEDLDELHALADRIAVMHAGHLT-EARPTAA 500


Lambda     K      H
   0.320    0.136    0.382 

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: 720
Number of extensions: 38
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 540
Length of database: 530
Length adjustment: 35
Effective length of query: 505
Effective length of database: 495
Effective search space:   249975
Effective search space used:   249975
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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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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:

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:

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:

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:

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