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 3607108 Dshi_0530 ABC transporter related (RefSeq)

Query= CharProtDB::CH_014279
         (504 letters)



>FitnessBrowser__Dino:3607108
          Length = 498

 Score =  299 bits (766), Expect = 1e-85
 Identities = 167/478 (34%), Positives = 271/478 (56%), Gaps = 3/478 (0%)

Query: 5   TPYLSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSV 64
           T ++  R I K + GV AL  + F    G+   L GENG+GKSTL+KI+SG    T G+V
Sbjct: 7   TAFIDLRAITKRYAGVTALDSVDFTVQPGEAVCLAGENGSGKSTLIKIISGVEPATAGTV 66

Query: 65  VINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENI-YLGQLPHKGGIVNRSLLNYE 123
            I GQE    +   +  AGV +I+Q+  L P ++VAENI +  QL  +  +     +   
Sbjct: 67  QIAGQEHVTLNPRISAAAGVMVIFQDFSLFPNLSVAENIAFTTQLSTRQRLFKFRAVRDI 126

Query: 124 AGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLF 183
           A   L  +G+ ID D  ++ L + Q Q+V I +ALA  A++I  DEPT++L+ +E+  L 
Sbjct: 127 ARAALDRIGVQIDLDARVETLPVAQKQLVAICRALASKAQLIIMDEPTTALTEKEVRRLQ 186

Query: 184 RVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGR 243
            +IR L++EG  +++VSH++ E+  +S+ + V ++G+ V       + D  +L   M GR
Sbjct: 187 GIIRMLKEEGVAVIFVSHKLAEVLEVSEKVVVLRNGKKVAE-GPASEFDTQSLTYHMTGR 245

Query: 244 DIGDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMF 303
           D+ ++      +  +  +++  +   G  + IS  +R+GE++G+ GL+G GR+ + K +F
Sbjct: 246 DVPEVPPSDVAAGAQTLMQVQGLGKAGSFSDISFDLRTGEVLGITGLLGCGRTSVAKALF 305

Query: 304 GGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKH 363
           G     AG + +D  P+ +  P  A  A +   PEDR  EG+    S+  N+ +     H
Sbjct: 306 GLVTPDAGSILVDGSPVPLGDPQAASLARIGYVPEDRLTEGLFLSQSILRNVAVGRLDAH 365

Query: 364 VLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILL 423
             GG +   G  +  +D  +R L +K P  E  + +LSGGNQQ+  L RWLS   +V++L
Sbjct: 366 TSGGFLDMTGLAKEASDW-LRRLKVKAPDVEAPVQSLSGGNQQRVALARWLSRAPRVLIL 424

Query: 424 DEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGEL 481
           + P+ G+DVG+K +I+++I  LA +G+ V+  S DLPE+L    R++VMREG I   L
Sbjct: 425 NGPSVGVDVGSKADIHDIIRELAREGIGVIVISDDLPELLATCHRVLVMREGRIIDAL 482


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: 560
Number of extensions: 25
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: 498
Length adjustment: 34
Effective length of query: 470
Effective length of database: 464
Effective search space:   218080
Effective search space used:   218080
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.

Links

Downloads

Related tools

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