GapMind for catabolism of small carbon sources

 

Alignments 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 3609459 Dshi_2843 ABC transporter related (RefSeq)

Query= CharProtDB::CH_014279
         (504 letters)



>FitnessBrowser__Dino:3609459
          Length = 548

 Score =  275 bits (702), Expect = 4e-78
 Identities = 176/508 (34%), Positives = 274/508 (53%), Gaps = 17/508 (3%)

Query: 6   PYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVV 65
           P +  RGI K F  V+A  DIS     G +H ++GENGAGKSTL+ IL G Y    G + 
Sbjct: 24  PAIELRGISKAFGPVQANKDISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADAGEIF 83

Query: 66  INGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAG 125
           I GQ+    D+ AA+ AG+ +++Q   LV   TV EN+ LG    +G ++  SL      
Sbjct: 84  IKGQKTEIPDSQAAIRAGIGMVFQHFKLVENFTVLENVVLG--AEEGALLRPSLAKARKL 141

Query: 126 LQ--LKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLF 183
           L+   +   +++ PD  ++ LS+G  Q VEI KAL R A I+  DEPT  L+  E D+LF
Sbjct: 142 LRELSEEYELNVAPDALIEDLSVGHQQRVEILKALYRKADILILDEPTGVLTPAEADHLF 201

Query: 184 RVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGR 243
           R++  L+ EG+ I+ ++H++ EI   +D ++V + G    T         + L + MVGR
Sbjct: 202 RILEGLKAEGKTIILITHKLREIMETTDTVSVMRRGEMTAT-VKTADTSPEQLAELMVGR 260

Query: 244 DIGDIYGWQPRSYGEERLRLD---AVKAPGVR--TPISLAVRSGEIVGLFGLVGAGRSEL 298
            +       P   G   L +D    V   GV     ISL VR+GE++G+ G+ G G+SEL
Sbjct: 261 KVLLRVDKTPAQPGAPILTVDDLRVVDDQGVERVKGISLQVRAGEVLGIAGVAGNGQSEL 320

Query: 299 MKGMFGGTQITAGQVYIDQQPIDIR-KPSHA---IAAGMMLCPEDRKAEGIIPVHSVRDN 354
           ++ + GG +   G+V +  Q ID+  K S+     A G+   PEDR+AEG+I  +   +N
Sbjct: 321 LE-VLGGMRPATGRVTVSGQQIDLTGKHSNGKTRRAQGIAHVPEDRQAEGLIMDYHAWEN 379

Query: 355 INISARRKHVLG-GCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRW 413
           +            G +++N     +A+  I   +++         N SGGNQQK +L R 
Sbjct: 380 VAFGYHDDPAYNRGLLMDNRAVRADAEGKIARFDVRPADCWLAAKNFSGGNQQKIVLARE 439

Query: 414 LSEEMKVILLDEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMR 473
           +    +++L+ +PTRG+D+GA   I+  I AL   G A+L  S +L E+L ++DR+ VM 
Sbjct: 440 IERNPELLLVGQPTRGVDIGAIEFIHQQIIALRDAGKAILLVSVELEEILSLSDRVAVMF 499

Query: 474 EGEIAGELLHEQADERQALSLAMPKVSQ 501
           +G I GE    + +E++ L L M  +++
Sbjct: 500 DGRIMGERPAAETNEKE-LGLLMAGITE 526


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: 684
Number of extensions: 38
Number of successful extensions: 10
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: 548
Length adjustment: 35
Effective length of query: 469
Effective length of database: 513
Effective search space:   240597
Effective search space used:   240597
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