GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araG in Photobacterium gaetbulicola Gung47

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate WP_044621444.1 H744_RS06405 ribose ABC transporter ATP-binding protein RbsA

Query= CharProtDB::CH_014279
         (504 letters)



>NCBI__GCF_000940995.1:WP_044621444.1
          Length = 501

 Score =  382 bits (981), Expect = e-110
 Identities = 213/500 (42%), Positives = 321/500 (64%), Gaps = 4/500 (0%)

Query: 6   PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVV 65
           P L  + I K FPGVKAL   S + Y G+V ALMGENGAGKSTL+K L+G Y    G + 
Sbjct: 4   PILELKDIEKAFPGVKALDKASLNVYPGKVMALMGENGAGKSTLMKALTGIYHMDAGEIR 63

Query: 66  INGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLG-QLPHKGGIVNRSLLNYEA 124
             GQ ++F+    +  AG++II+QEL+L+PE+T+AENI+LG +  +  G +  S +  EA
Sbjct: 64  YQGQTVNFNGPRHSQEAGISIIHQELNLIPELTIAENIFLGREKTNAFGGIKWSQMYKEA 123

Query: 125 GLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFR 184
              L  L +     T L  LS+G+ QMVEIAKAL+  +++I  DEPT +L+  E ++LF+
Sbjct: 124 DALLARLNVKHSSRTLLGDLSLGEQQMVEIAKALSFKSQVIIMDEPTDALTDTETESLFK 183

Query: 185 VIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRD 244
           VI ELR+EG  I+Y+SHR++EIF + D ITV +DG+++     +  +D D +++ MVGR 
Sbjct: 184 VINELREEGTGIVYISHRLKEIFEICDDITVLRDGKFIGQRA-VADIDEDTMIEMMVGRR 242

Query: 245 IGDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFG 304
           + + Y      +G   L +  +  PGV   +S  +  GEI+G+ GL+GAGR+ELMK ++G
Sbjct: 243 LDEQYPRIDVKHGTTCLAVKNLNGPGVHD-VSFTLDRGEILGISGLMGAGRTELMKVIYG 301

Query: 305 GTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHV 364
             +  +G V +D + I+   P   +A G+    EDRK +G+I   SV++N++I +  + +
Sbjct: 302 ALERESGDVVLDGKVINPLTPQDGLANGIAYISEDRKGDGLILGLSVKENMSICSLEQ-L 360

Query: 365 LGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLD 424
             G  + +  E    +  IR  NIKTP   Q+I NLSGGNQQK  + + L  + KV++LD
Sbjct: 361 SKGIQLRHYDEVTAVEDFIRLFNIKTPTHNQIIGNLSGGNQQKVAIAKGLMTKPKVLILD 420

Query: 425 EPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHE 484
           EPTRG+DVGAK EIY +I    ++G++++  SS++PEVLG++DRI+VM EG+I+GE + E
Sbjct: 421 EPTRGVDVGAKKEIYQLINQFKSEGMSIILVSSEMPEVLGMSDRILVMHEGKISGEFMAE 480

Query: 485 QADERQALSLAMPKVSQAVA 504
           +AD+ + L+ A+ K    VA
Sbjct: 481 EADQEKLLACAVGKQINEVA 500


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: 706
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: 501
Length adjustment: 34
Effective length of query: 470
Effective length of database: 467
Effective search space:   219490
Effective search space used:   219490
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