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 GFF1451 HP15_1416 L-carnitine dehydratase/bile acid-inducible protein F

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



>FitnessBrowser__Marino:GFF1451
          Length = 401

 Score =  228 bits (581), Expect = 2e-64
 Identities = 136/406 (33%), Positives = 212/406 (52%), Gaps = 18/406 (4%)

Query: 2   GALSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTT 61
           G L  +R++DL+ +++GP A  ILAD GA+VIK+E P  GD TR+        A      
Sbjct: 3   GPLDGIRIIDLTAMISGPLATMILADQGAEVIKIENPAGGDFTRS--------AANRQGD 54

Query: 62  EAAYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAI 121
            +A YL+ NRNK+SV ++  +  G+  +  L A +D+ ++NF+ G +   GL  + L+ +
Sbjct: 55  MSALYLNNNRNKKSVALNLKKKAGRDALLRLVASADVFVQNFRPGVIERMGLGEEQLRKV 114

Query: 122 NPQLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDIL 181
            P L+  SI+GFG TGPY++R  YD +IQGL GL ++     G +   P  V   L D L
Sbjct: 115 APNLVMVSISGFGDTGPYSQRPVYDPLIQGLSGLATVQA---GADELRPQLVRTILPDKL 171

Query: 182 TGLYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLT--TGNAPKRLGNAH 239
           TG+ +  AI AAL  R+  G  QH+ +++LD  +A L +  M   T      P++   + 
Sbjct: 172 TGVTAAQAITAALFARERTGESQHVRLSMLDAIIAFLWSSDMGSQTFVHSEVPQQEAASL 231

Query: 240 PNIVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPL 299
            +++    + T  G   + V +D +++       +P+WA+DPRF T ++R  N    + L
Sbjct: 232 QDLI----YETTTGYITIAVQSDREWQALIRAVDRPEWAEDPRFLTARLRQENIDARLEL 287

Query: 300 IRQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELPHLLAGKVPQVA 359
           I+      T   W+ +LE   VPC P+    QV   PQV A  L     H  AG++ Q  
Sbjct: 288 IQSVIKTDTAEHWLARLEAEQVPCAPVLTRTQVLDHPQVLANDLLSHYDHPQAGRLRQAR 347

Query: 360 SPIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGV 405
           +P R S  P ++    P LGE T E+L    G     + A  ++G+
Sbjct: 348 APSRFSAAPEQHWQGAPRLGEQTGELLAE-CGYSAEEIQAMCDSGI 392


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: 435
Number of extensions: 29
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: 401
Length adjustment: 31
Effective length of query: 375
Effective length of database: 370
Effective search space:   138750
Effective search space used:   138750
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