GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araG in Rhodobacter johrii JA192

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>NCBI__GCF_003046325.1:WP_069332735.1
          Length = 499

 Score =  337 bits (863), Expect = 8e-97
 Identities = 191/491 (38%), Positives = 291/491 (59%), Gaps = 4/491 (0%)

Query: 6   PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVV 65
           P L+ R + + F  V+ L D+ FD   G+VHAL+GENGAGKST +KIL+G  AP+ G V+
Sbjct: 4   PVLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVL 63

Query: 66  INGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAG 125
           ++G+ + F  +  A  AGV +I+QE +L   +TV ENI+LG+   +G  ++   +  E+ 
Sbjct: 64  LDGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKRGPFLDHRAMQAESR 123

Query: 126 LQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRV 185
             L+ L   +DP   +  LS+   QMVEIAKAL   A+++  DEPT+ L+ RE D L   
Sbjct: 124 RLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLLEQ 183

Query: 186 IRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDI 245
           +  LR  G  ILY SH+++E+  ++D +TV +DGR V T    + +  D + + MVGR++
Sbjct: 184 VDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMT-APAKGLSEDRMAETMVGREL 242

Query: 246 GDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGG 305
             ++  +     E  L +  +  PG     S  +R GE++G  GLVG+GR+ELM+G+ G 
Sbjct: 243 SGLFPPKSSPAPEPVLEVAGLTVPGFVRDASFTLRRGEVLGFAGLVGSGRTELMEGIVGL 302

Query: 306 TQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHVL 365
              T G+V ++  P+     S A AAG++   EDRK +G++    + +N+ + A  +   
Sbjct: 303 RPAT-GEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTLLALDR--F 359

Query: 366 GGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLDE 425
           G  +I+   EE      I   +I+         +LSGGNQQK +L + +  E +V+++DE
Sbjct: 360 GRVLIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAEPRVVIIDE 419

Query: 426 PTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHEQ 485
           PTRGIDVG K +IY  I  LAA+G +V+  SS+LPEV+G+A+R+VVM  G IAGE+  E 
Sbjct: 420 PTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRIAGEVEGEA 479

Query: 486 ADERQALSLAM 496
             E   + LAM
Sbjct: 480 ITEENIVRLAM 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: 626
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: 499
Length adjustment: 34
Effective length of query: 470
Effective length of database: 465
Effective search space:   218550
Effective search space used:   218550
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 24 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