GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araG in Bradyrhizobium sp. BTAi1

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate WP_012042345.1 BBTA_RS09915 sugar ABC transporter ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>NCBI__GCF_000015165.1:WP_012042345.1
          Length = 516

 Score =  332 bits (852), Expect = 1e-95
 Identities = 181/480 (37%), Positives = 298/480 (62%), Gaps = 10/480 (2%)

Query: 8   LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67
           L  RG+ K+F  +KAL D+ F    G++HAL+GENGAGKSTL+K+++G +A   G+V + 
Sbjct: 15  LEIRGLTKSFGALKALQDVDFTLGEGEIHALLGENGAGKSTLIKVVTGVFARDAGTVRLA 74

Query: 68  GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127
           G E++      A+ AG+A +YQE++L+P ++VA+N+YLG+ P + G+V ++ +   A   
Sbjct: 75  GDEIAPRSAKDAVEAGIATVYQEVNLLPNLSVAQNLYLGRQPTRFGVVRQAEMRRRAHAL 134

Query: 128 LKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIR 187
           L   G+DID   PL   S+    +  IA+A+  +A+++  DEPT+SL   E++ LFRV+R
Sbjct: 135 LLDYGLDIDVGAPLASYSVAVQHITAIARAVDLSARVLILDEPTASLDRHEVEILFRVMR 194

Query: 188 ELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKT--FTDMQQVDHDALVQAMVGRDI 245
           +L  +G  I++VSH +++++ + D +TV ++GR + T   TD+ ++D   L++ M+GR++
Sbjct: 195 KLAADGIGIVFVSHFLDQVYEICDRVTVLRNGRLIGTRDITDLPRLD---LIRMMLGREL 251

Query: 246 GDI----YGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKG 301
            +        QP +  E  +        G   P  L +R GE+VGL GL+G+GR+E  + 
Sbjct: 252 AETTHERAASQPDTAREVCVSFKGFGKQGYVAPFDLELRRGEVVGLAGLLGSGRTETARL 311

Query: 302 MFGGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARR 361
           +FG  +  +G+  +  + + +  P  A   G   CPE+RK EGI+   +VR+NI ++ + 
Sbjct: 312 VFGAERADSGEASVAGKAVRLNSPRDAAGLGFGYCPEERKTEGIVADLTVRENIVLALQA 371

Query: 362 KHVLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVI 421
           +  L    ++   ++  A  +IR L+I+ P  E+ I  LSGGNQQKA+L RWL+   K++
Sbjct: 372 RRGLHR-PLSRREQDEIAMRYIRMLDIRPPDPERPIGLLSGGNQQKALLARWLATSPKLL 430

Query: 422 LLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGEL 481
           +LDEPTRGIDVGA  EI  ++  L  QG+A+L  SS+L E++  ++R+VV+R+     EL
Sbjct: 431 VLDEPTRGIDVGAHAEIIRLVRDLCEQGLALLVISSELDEIVTYSNRVVVLRDRAHVEEL 490


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: 631
Number of extensions: 28
Number of successful extensions: 7
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: 516
Length adjustment: 34
Effective length of query: 470
Effective length of database: 482
Effective search space:   226540
Effective search space used:   226540
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 Apr 09 2024. 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