GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Marinobacter adhaerens HP15

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate GFF2665 HP15_2609 acyl-CoA transferase/carnitine dehydratase

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



>FitnessBrowser__Marino:GFF2665
          Length = 398

 Score =  260 bits (664), Expect = 6e-74
 Identities = 143/391 (36%), Positives = 222/391 (56%), Gaps = 9/391 (2%)

Query: 4   LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63
           L  +R++DL+ +L+GP+AG +LAD+GA+ IKVE P  G+ TR+      KD R       
Sbjct: 5   LEGVRIIDLTHMLSGPYAGMLLADMGAESIKVE-PLKGEGTRSL---LAKDPRNSYNGHG 60

Query: 64  AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123
           AY+++ NRNK+SV ID     G +   +L   +DI+++NF  G  A   +D++ L  +NP
Sbjct: 61  AYFITLNRNKKSVCIDLKSEAGLQTFYDLVKDADIVLDNFSAGVPAKLKIDHEHLSRVNP 120

Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183
           ++I CS+TGFGQ GP  KR  +D ++QG+GG MS+TG     +   P + G+ + D+  G
Sbjct: 121 RIITCSVTGFGQAGPNFKRPAFDQVVQGIGGGMSITGH----DAEHPARAGIPIGDLGGG 176

Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243
           +++   +LAAL  R   G GQH+D+++LD Q++ L   A  Y  +G+ P  +GN H   V
Sbjct: 177 MFAVMGVLAALHSRAVNGYGQHVDISMLDCQISMLNYMATMYFLSGDNPSPIGNGHFVHV 236

Query: 244 PYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQA 303
           PY  F T++G  I+ V  D  +    E+ G  +   DP + T   R A++  +  ++   
Sbjct: 237 PYDAFRTSNGFVIIAVIFDSFWDNLVELLGIDE-LRDPAYKTQPGRFADKHKINGILTDL 295

Query: 304 TVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVASPIR 363
               TT  WV  L  A +PC P+N  +   +DPQV  R + +++P    G V    +PI+
Sbjct: 296 LKTNTTEHWVELLSSARIPCAPVNKFSDALSDPQVLFRNMVVDIPQFDGGTVKAPGNPIK 355

Query: 364 LSETPVEYRNAPPLLGEHTLEVLQRVLGLDE 394
           LS    +   APPLLG+HT +VL+ +   DE
Sbjct: 356 LSVDSSDSYTAPPLLGQHTEDVLKSLGYSDE 386


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: 449
Number of extensions: 22
Number of successful extensions: 4
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: 398
Length adjustment: 31
Effective length of query: 375
Effective length of database: 367
Effective search space:   137625
Effective search space used:   137625
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