GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garK in Sinorhizobium meliloti 1021

Align D-glycerate 2-kinase (EC 2.7.1.-) (characterized)
to candidate SMc04389 SMc04389 hydroxypyruvate reductase

Query= reanno::psRCH2:GFF1145
         (423 letters)



>FitnessBrowser__Smeli:SMc04389
          Length = 455

 Score =  381 bits (979), Expect = e-110
 Identities = 207/420 (49%), Positives = 273/420 (65%), Gaps = 3/420 (0%)

Query: 2   TLDPQALLRQLFDSAIEAAHPRHVLADHLPEDRSGRAIVIGAGKAAAAMAEAIEKVWEGE 61
           +++P+  L  LF++A+ AA P   +  HLP    GR IV+GAGKAA+ MA A E++W+G 
Sbjct: 35  SIEPRPFLISLFEAAVAAADPEAAIRAHLPARPKGRTIVVGAGKAASQMAAAFERLWDGP 94

Query: 62  LSGLVVTRYEHHADCKRIEVVEAAHPVPDDAGERVARRVLELVSNLEESDRVIFLLSGGG 121
           L+G VV R+     C RI V+++AHPVPD+AG   +  +LE V  L   D V+ L+SGGG
Sbjct: 95  LAGAVVARHGPVEKCGRIRVLQSAHPVPDEAGLAASAALLETVGGLTADDLVVALISGGG 154

Query: 122 SSLLALPAEGISLADKQAINKALLRSGAHIGEMNCVRKHLSAIKGGRLAKACWPASVYTY 181
           S+LL  P  G++L D+ A+NKALL SGA I  MN VRKH+S IKGGRLA A  PA V + 
Sbjct: 155 SALLPAPPGGLTLEDEIAVNKALLASGAPISAMNVVRKHVSRIKGGRLALAAAPARVVSL 214

Query: 182 AISDVPGDEATVIASGPTVADPTTSEQALEILERYHIEVPANVRAWLEDPRSETLKPGDP 241
            +SDVPGD    +ASGPTVAD ++ E+A EI+ RY I +P  V A L    +   +P D 
Sbjct: 215 VVSDVPGDNPAFVASGPTVADRSSLEEAREIVARYAIALPERVTAHLASDAARAPRPDDA 274

Query: 242 MLSRSHFRLIATPQQSLDAAAEVARAAGITPLILGD-LEGEAREVAKVHAGIARQVVLHG 300
             + +   +IA+   SL+AAA  AR +GI  +IL D +EGEAR++ ++HA +AR+V    
Sbjct: 275 AFAGNEVHVIASASVSLEAAAARARESGIEAMILSDAIEGEARDIGRMHAALAREVASRN 334

Query: 301 QPIAAPCVILSGGETTVTVRGN--GRGGRNAEFLLALTENLQGLPNVYALAGDTDGIDGS 358
           +P + P V+LSGGETTVT+ G   G+GGRN+EFLL+L  ++ G+  + ALA DTDGIDGS
Sbjct: 335 RPFSKPVVLLSGGETTVTISGERYGKGGRNSEFLLSLALDIDGIGGIDALAADTDGIDGS 394

Query: 359 EDNAGALMMPDSYARAETLGLRAADALANNDGYGYFAALDDLIVTGPTRTNVNDFRAILI 418
           EDNAGA     S  R    G      LA +D +  FAA  DL V GPT TNVND RAILI
Sbjct: 395 EDNAGAFADGASIGRMRAAGADPRSHLAGHDAWTAFAASGDLFVPGPTGTNVNDLRAILI 454


Lambda     K      H
   0.316    0.134    0.384 

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: 510
Number of extensions: 23
Number of successful extensions: 3
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: 423
Length of database: 455
Length adjustment: 32
Effective length of query: 391
Effective length of database: 423
Effective search space:   165393
Effective search space used:   165393
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 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