GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garD in Sinorhizobium meliloti 1021

Align L-talarate dehydratase (EC 4.2.1.156); galactarate dehydratase (EC 4.2.1.42) (characterized)
to candidate SMa1351 SMa1351 enolase

Query= BRENDA::Q8ZL58
         (398 letters)



>FitnessBrowser__Smeli:SMa1351
          Length = 402

 Score =  142 bits (358), Expect = 2e-38
 Identities = 110/356 (30%), Positives = 176/356 (49%), Gaps = 32/356 (8%)

Query: 57  LTEVAIIIAEIRSRDGFEG--VGFSYSKRAGGQGIYAHAK--EIADNLLGEDPNDIDKIY 112
           LT     I  I + DG  G   G + +  AG  G   H    E+   L+G D  DI  ++
Sbjct: 41  LTTFDAAILRIETDDGIVGWGEGKNAAGSAGSYGTLVHMLNYEVGPRLVGRDAADISAVW 100

Query: 113 TKLLWAGA-------------SVGRSGMAVQAISPIDIALWDMKAKRAGLPLAKLLGAHR 159
            ++L+ G               + R G+++ AIS +DIALWD+  K  G+P+ KLLG  +
Sbjct: 101 -EMLYNGVRHERAAMSGHAMPELSRRGLSIAAISAVDIALWDILGKSLGVPVWKLLGGRK 159

Query: 160 -DSVQCYNTSGGFLHTPLDQVLKNVVISRENGIGGIKLKVGQPNCAEDIR--RLTAVREA 216
            D +  Y + G      +   L++ + S   G   +K++VG  + A  +   R+ A R+A
Sbjct: 160 ADRLPAYASGGWESAEKIGGQLQSYLAS--GGFKAVKMRVGAMDGAPYVSAARVRAARKA 217

Query: 217 LGDEFPLMVDANQQWDRETAIRMGRKMEQFNLIWIEEPLDAYDIEGHAQLAAALDTPIAT 276
           LG    +MVDA+  +    A R  + +   +L W EEP+ A D  G A++ AA + PIAT
Sbjct: 218 LGPSVDIMVDAHGTYTVADAKRFIQLVRDCDLAWFEEPVIADDKAGMAEVRAAGNVPIAT 277

Query: 277 GEMLTSFREHEQLILGNASDFVQPDAPRVGGISPFLKIMDLAAKHGRKLAPHF-----AM 331
           GE   +      L +  ++D  QPD    GGI+  ++I  +A+    +LAPH        
Sbjct: 278 GESEATRFAFRDLAVLRSADIFQPDPAFCGGITEAMRIGAIASAFNLRLAPHLWAGAPCF 337

Query: 332 EVHLHLSAAYPLEPWLEHFEWLNPLFNEQLE----LRDGRMWISDRHGLGFTLSEQ 383
              LH+ AA P    +E+    NP+ ++ +E    ++DG + I D+ GLGFT++E+
Sbjct: 338 FSGLHICAASPASFVVEYSVGANPMIHDLVEETVAVKDGMLEIPDKPGLGFTINER 393


Lambda     K      H
   0.319    0.136    0.410 

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: 400
Number of extensions: 21
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: 398
Length of database: 402
Length adjustment: 31
Effective length of query: 367
Effective length of database: 371
Effective search space:   136157
Effective search space used:   136157
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 (21.8 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