GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araG in Cupriavidus basilensis 4G11

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate RR42_RS03360 RR42_RS03360 sugar ABC transporter ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>FitnessBrowser__Cup4G11:RR42_RS03360
          Length = 537

 Score =  373 bits (958), Expect = e-108
 Identities = 224/489 (45%), Positives = 301/489 (61%), Gaps = 17/489 (3%)

Query: 6   PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNY-APTTGSV 64
           P L+ R I KTFPGV+AL  +    YAG+VHALMGENGAGKSTL+KILSG Y A   G  
Sbjct: 9   PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 68

Query: 65  VINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEA 124
            I+GQ +      +A + GVA+IYQEL L P ++VAENIYLG+   + G+V R  +    
Sbjct: 69  HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 128

Query: 125 GLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFR 184
              L  LG D  P   +  LSI Q Q+VEIA+A+   A+I+  DEPT+ LS  E D LF 
Sbjct: 129 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 188

Query: 185 VIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRD 244
           +IR+LR EG  ILY+SHRM EI  L+D +TV +DG +V T  D   +   ALV+ MVGRD
Sbjct: 189 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTL-DRAHLSQAALVKMMVGRD 247

Query: 245 IGDIYGWQPRSYGE--ERLRLDAVK--APGVRTP-ISLAVRSGEIVGLFGLVGAGRSELM 299
           +    G+  +++G+  ER  + +V+  A G R    S  +R+GE++GL GLVGAGR+EL 
Sbjct: 248 LS---GFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELA 304

Query: 300 KGMFGGTQITAGQVYIDQQ-------PIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVR 352
           + +FG    T G+V I           +    P  AI AG+    EDRK +G+    SV 
Sbjct: 305 RLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVH 364

Query: 353 DNINISARRKHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGR 412
           +NIN+    +  LG   +N           I +L I+   A+  +  LSGGNQQK +L R
Sbjct: 365 ENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSR 424

Query: 413 WLSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVM 472
            L  + +V++LDEPTRG+D+GAK EIY +I ALA  GVA+L  SS+LPEV+G+ DR++VM
Sbjct: 425 LLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVM 484

Query: 473 REGEIAGEL 481
           REG +AGE+
Sbjct: 485 REGTLAGEV 493


Lambda     K      H
   0.319    0.136    0.391 

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: 679
Number of extensions: 36
Number of successful extensions: 9
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: 504
Length of database: 537
Length adjustment: 35
Effective length of query: 469
Effective length of database: 502
Effective search space:   235438
Effective search space used:   235438
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 (21.7 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