GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PGA1_c07320 in Dyella japonica UNC79MFTsu3.2

Align Inositol transport system ATP-binding protein (characterized)
to candidate N515DRAFT_3232 N515DRAFT_3232 xylose ABC transporter ATP-binding protein

Query= reanno::Phaeo:GFF717
         (261 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3232
          Length = 513

 Score =  152 bits (384), Expect = 1e-41
 Identities = 91/243 (37%), Positives = 140/243 (57%), Gaps = 7/243 (2%)

Query: 7   LIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGV--HKPTKGDI 64
           L  M+GI K FG V AL G+ + +  GEC  L G+NGAGKST +K +SGV  H    G+I
Sbjct: 7   LFEMRGIAKSFGGVKALDGIDLRLRAGECLGLCGENGAGKSTLMKVLSGVYPHGSWDGEI 66

Query: 65  LFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYA 124
           L++GQPL     RD+  AGI  +HQ L ++P +SV+ N F+G+E  R  G +  +D  YA
Sbjct: 67  LWQGQPLRARSVRDSERAGIVIIHQELMLVPQLSVAENIFLGHEITRPGGRMD-YDAMYA 125

Query: 125 NR-ITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQ 183
                ++E+    +N+  P    G   GG +Q   IA+A+   AK+LILDEPTS+L   +
Sbjct: 126 KADALLQELGLHDVNVALPAMHYG---GGHQQLFEIAKALAKQAKLLILDEPTSSLTSSE 182

Query: 184 TANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEELQDM 243
           T  +L  ++ ++++GVA ++I+H +     V D   V+  G+ + T    ++  + L  +
Sbjct: 183 TEVLLGIVEDLKRRGVACIYISHKLDEVERVCDTVCVIRDGRHIATQPMHELDVDTLITL 242

Query: 244 MAG 246
           M G
Sbjct: 243 MVG 245



 Score = 82.0 bits (201), Expect = 2e-20
 Identities = 63/229 (27%), Positives = 102/229 (44%), Gaps = 26/229 (11%)

Query: 26  VSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKGDILF-EGQPLHFADPRDAIAAGI 84
           VS  +  GE   + G  GAG++  +  + G +       LF EG+PL    P DAI AG+
Sbjct: 285 VSFQLRRGEILGIAGLVGAGRTELVSAIFGAYTGKSSVELFLEGRPLKIRSPADAIRAGL 344

Query: 85  ATV---HQHLAMIPLMSVSRNFFMGNEPIRKIGPLKLFDHDYANRITMEEMRKM------ 135
             V    +   ++PL+ V  N             L   DH YA+   ++  R++      
Sbjct: 345 GMVPEDRKRHGIVPLLGVGDNI-----------TLATLDH-YAHAGHIDRQRELVAIEAQ 392

Query: 136 ----GINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTSALGVRQTANVLATI 191
                +    P   +  LSGG +Q   +A+ +    KVLILDEPT  + V   A +   I
Sbjct: 393 IAERRVKTASPALPIARLSGGNQQKAVLAKMLLARPKVLILDEPTRGVDVGAKAEIYRLI 452

Query: 192 DKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISAEEL 240
            ++  QGVA+V ++  +   L + DR  V+  G+  G      ++ E++
Sbjct: 453 FELAAQGVAIVLVSSEMPEVLGMADRVLVMGEGRLRGDFPNQGLTQEQV 501


Lambda     K      H
   0.321    0.137    0.395 

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: 349
Number of extensions: 22
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 261
Length of database: 513
Length adjustment: 29
Effective length of query: 232
Effective length of database: 484
Effective search space:   112288
Effective search space used:   112288
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 (21.9 bits)
S2: 49 (23.5 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