Aligments for a candidate for araG in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Aligments for a candidate for araG in Dinoroseobacter shibae DFL-12

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)

Query= CharProtDB::CH_014279
         (504 letters)



>lcl|FitnessBrowser__Dino:3609044 Dshi_2433 ABC transporter related
           (RefSeq)
          Length = 510

 Score =  360 bits (924), Expect = e-104
 Identities = 194/477 (40%), Positives = 299/477 (62%), Gaps = 7/477 (1%)

Query: 8   LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67
           L+   I KTFPGVKAL+D+S   Y G+V AL+GENGAGKST++KIL+G Y P  G ++++
Sbjct: 21  LALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKILTGIYQPDGGRILVD 80

Query: 68  GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKG-GIVNRSLLNYEAGL 126
           GQ + FS   AA + GV  I+QE  L  E++VAENI+LG  P    G+++       A  
Sbjct: 81  GQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGAFGLIDWKKTTENARA 140

Query: 127 QLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVI 186
            L  +G ++DPD  LK L I    +V IA+AL+  A+++  DEPT++LS +EI+ L+ ++
Sbjct: 141 LLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPTAALSHKEIEELYELV 200

Query: 187 RELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVK--TFTDMQQVDHDALVQAMVGRD 244
             L+ +G+ IL++SH+ +EIF ++D  TVF+DG+ +      D+ + D   LV+ MVGRD
Sbjct: 201 ESLKAQGKAILFISHKFDEIFRIADNYTVFRDGQLIGDGAIADVTEAD---LVKMMVGRD 257

Query: 245 IGDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFG 304
           +  I+  +  + G+  L +     P     IS  +R GEI+G +GLVGAGRSE M+ +FG
Sbjct: 258 VSQIFPQRAPNVGDTVLTVQGYAHPTEFDDISFTLREGEILGFYGLVGAGRSEFMQSLFG 317

Query: 305 GTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHV 364
            T+ +AG V I     +I  P+ A+  G++  PEDR  +G I    +  N+ + +  +  
Sbjct: 318 ITRPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPIFQNVTLPSLGRIS 377

Query: 365 LGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLD 424
             G  +    E   A  +   L+++    +  + NLSGGNQQK ++ +WL+   +VI+LD
Sbjct: 378 RKG-FLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAKWLATRPRVIILD 436

Query: 425 EPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGEL 481
           EPT+G+D+G+K  +++ +  LAAQG+AV+  SS++PEVLG++DR++VMREG I  EL
Sbjct: 437 EPTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVMREGRIVAEL 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: 675
Number of extensions: 37
Number of successful extensions: 8
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: 510
Length adjustment: 34
Effective length of query: 470
Effective length of database: 476
Effective search space:   223720
Effective search space used:   223720
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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources