GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Paraburkholderia bryophila 376MFSha3.1

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate H281DRAFT_03364 H281DRAFT_03364 Crotonobetainyl-CoA:carnitine CoA-transferase CaiB

Query= reanno::pseudo5_N2C3_1:AO356_10845
         (406 letters)



>FitnessBrowser__Burk376:H281DRAFT_03364
          Length = 407

 Score =  264 bits (675), Expect = 3e-75
 Identities = 148/405 (36%), Positives = 222/405 (54%), Gaps = 14/405 (3%)

Query: 1   MGALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENT 60
           +G LS  R+LDL+ + AGP    +LADLGADV+KVE P  GD +R  G  F++       
Sbjct: 6   VGPLSGYRILDLTVMTAGPVGTVLLADLGADVVKVEEPMAGDLSRKLGNQFVQG------ 59

Query: 61  TEAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKA 120
            E+  +LS NRNK+S+ +D   P+G+     +A ++D+++ENF+ G +   G+ Y ++KA
Sbjct: 60  -ESVQFLSQNRNKRSIRLDLKSPKGRDAFLRMAEQADVVVENFRPGTVDRLGIGYAAVKA 118

Query: 121 INPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDI 180
            NP+++Y S++ FGQ+GPYA     D ++Q + GLM +T    G+ G  PV++G  L D 
Sbjct: 119 RNPKIVYASVSAFGQSGPYAAWPANDPIVQAVAGLMDMT----GEAGGNPVRLGAPLPDF 174

Query: 181 LTGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHP 240
                    I AAL HR+  G GQ ID +LL   +     +    L +G AP+RLG+ HP
Sbjct: 175 GAAALLAFGISAALLHRERHGEGQRIDTSLLSAALFSTIPRDGETLRSGKAPERLGSGHP 234

Query: 241 NIVPYQDFPTADGDFILTVGNDGQF-RKFAEVAGQPQWADDPRFATNKVRVANRAVLIPL 299
            +VPY+++  +DG +        +F +      G+ +   D RF  N  R ANR  L  +
Sbjct: 235 TMVPYRNYQGSDGRYFFAACFTEKFWQNLCRALGREELLSDERFIGNTARTANRHALDVI 294

Query: 300 IRQATVFKTTAEWVTQLEQAGVPCGPINDL-AQVFADPQVQARGLAMELPHLLAGKVPQV 358
           + +  +  T   WV  L  A VPC  + D    +  DPQ+      +E+ H +AG+V  +
Sbjct: 295 LEEQFLLHTAEYWVAHLSAADVPCAIVQDYHTALTQDPQISHNHAVVEIEHPVAGRVTNI 354

Query: 359 ASPIRLSETPVEYRNAPPLLGEHTLEVLQRV-LGLDEAAVMAFRE 402
           ASP+    +PV YR  PP LG+HT EVL     G +E A +  RE
Sbjct: 355 ASPVNFHGSPVAYRRPPPTLGQHTAEVLAEYGFGEEEIAALEGRE 399


Lambda     K      H
   0.319    0.137    0.408 

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: 474
Number of extensions: 20
Number of successful extensions: 5
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: 406
Length of database: 407
Length adjustment: 31
Effective length of query: 375
Effective length of database: 376
Effective search space:   141000
Effective search space used:   141000
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: 50 (23.9 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