GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araG in Pseudomonas fluorescens FW300-N2C3

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate AO356_23205 AO356_23205 D-ribose transporter ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_23205
          Length = 517

 Score =  382 bits (982), Expect = e-110
 Identities = 202/492 (41%), Positives = 315/492 (64%), Gaps = 4/492 (0%)

Query: 6   PYL-SFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSV 64
           PYL     + K FPGV AL+D+      G V ALMGENGAGKSTL+KI++G Y P  G +
Sbjct: 24  PYLLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGEL 83

Query: 65  VINGQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKG-GIVNRSLLNYE 123
            + G+ ++F    AAL AG+A+I+QEL+L+P M++AENI++G+    G  +V+   ++  
Sbjct: 84  RLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMVDHGEMHRC 143

Query: 124 AGLQLKHLGMDIDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLF 183
               L+ L + +DP+  +  LSI + QMVEIAKA++ ++ I+  DEPTS+++  E+ +LF
Sbjct: 144 TARLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLF 203

Query: 184 RVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGR 243
            +I +L+ +G+ I+Y++H+M E+FA++D + VF+DG Y+        +D D+L+  MVGR
Sbjct: 204 SIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIG-LQRADSMDGDSLISMMVGR 262

Query: 244 DIGDIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMF 303
           ++  ++  + +  GE  L +  +   G+   +S  + +GEI+G+ GL+G+GR+ + + +F
Sbjct: 263 ELSQLFPVREQPIGELVLSVRDLSLDGIFKGVSFDLHAGEILGIAGLMGSGRTNVAEAIF 322

Query: 304 GGTQITAGQVYIDQQPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKH 363
           G T  T G++ +D QP+ I  P  AI  G  L  EDRK  G+ P  SV +N+ ++    H
Sbjct: 323 GVTPSTGGEIRLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVL-PH 381

Query: 364 VLGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILL 423
            +G   I         +   + L +KTP  EQ I  LSGGNQQKA+L RWL    ++++L
Sbjct: 382 YVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRILIL 441

Query: 424 DEPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLH 483
           DEPTRGIDVGAK EIY +I  LA++G+AV+  SS+LPEVLG++DR++VM EG++ G L  
Sbjct: 442 DEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGTLDR 501

Query: 484 EQADERQALSLA 495
            +A + + + LA
Sbjct: 502 SEATQERVMQLA 513


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: 647
Number of extensions: 25
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: 517
Length adjustment: 35
Effective length of query: 469
Effective length of database: 482
Effective search space:   226058
Effective search space used:   226058
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