GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garK in Dinoroseobacter shibae DFL-12

Align D-glycerate 2-kinase (EC 2.7.1.-) (characterized)
to candidate 3609663 Dshi_3046 Hydroxypyruvate reductase (RefSeq)

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



>FitnessBrowser__Dino:3609663
          Length = 415

 Score =  419 bits (1077), Expect = e-122
 Identities = 230/420 (54%), Positives = 280/420 (66%), Gaps = 9/420 (2%)

Query: 1   MTLDPQALLRQLFDSAIEAAHPRHVLADHLPEDRSGRAIVIGAGKAAAAMAEAIEKVWEG 60
           M  DP+  LR LF +A+ AA P   + + LP   +GR +V+GAGKA+A MA+A+E  W G
Sbjct: 1   MIADPEPFLRGLFRAAVAAADPGLAVPNFLPAKPAGRVVVVGAGKASAKMAQAVEAAW-G 59

Query: 61  ELSGLVVTRYEHHADCKRIEVVEAAHPVPDDAGERVARRVLELVSNLEESDRVIFLLSGG 120
              G+V+  Y      + IE+VEA HPVPD AGE  A R+L LVS L E D  + L+SGG
Sbjct: 60  PCEGIVIVPYGGALPTEGIEIVEARHPVPDAAGEAAAGRILNLVSGLGEGDLALCLISGG 119

Query: 121 GSSLLALPAEGISLADKQAINKALLRSGAHIGEMNCVRKHLSAIKGGRLAKACWPASVYT 180
           GS+L+A P EG++LADKQA+NKALL  GA I EMNC+RKHLS IKGGRL  A WPA   T
Sbjct: 120 GSALMAAPGEGLTLADKQAVNKALLSCGAAIDEMNCLRKHLSRIKGGRLTVAAWPARTVT 179

Query: 181 YAISDVPGDEATVIASGPTVADPTTSEQALEILERYHIEVPANVRAWLEDPRSETLKPGD 240
             ISDVPGD+  +IASGPTVADPTT+ +A  I  RYH+ +   V A+L+ P +ET  P  
Sbjct: 180 LTISDVPGDDPAIIASGPTVADPTTATEARAIAARYHLALSDAVAAYLQTPAAETPDPSH 239

Query: 241 PMLSRSHFRLIATPQQSLDAAAEVARAAGITPLILGD-LEGEAREVAKVHAGIARQVVLH 299
           P  + +   LIATPQ +L+AAA  ARA G+TPLILGD LEGEA E+  V AGIAR  V H
Sbjct: 240 PAFAAAECHLIATPQMALEAAAATARAEGVTPLILGDALEGEAAELGIVLAGIARAAVTH 299

Query: 300 GQPIAAPCVILSGGETTVTVRGN-GRGGRNAEFLLALTENLQGLPNVYALAGDTDGIDGS 358
           G P+  P V+LSGGETTVTVRG  GRGGRN+E LL+    L     V A+A DTDGIDGS
Sbjct: 300 GHPVTGPAVLLSGGETTVTVRGGAGRGGRNSECLLSF--GLHAPEGVSAIACDTDGIDGS 357

Query: 359 EDNAGALMMPDSYARAETLGLRAADALANNDGYGYFAALDDLIVTGPTRTNVNDFRAILI 418
           EDNAGAL +P    R       A   L  +D Y +F     L+V+GPT TNVNDFRA+ I
Sbjct: 358 EDNAGALWVP----RVAAHKAEARKYLEAHDAYSFFEKAGGLVVSGPTHTNVNDFRAVYI 413


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: 523
Number of extensions: 23
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: 423
Length of database: 415
Length adjustment: 32
Effective length of query: 391
Effective length of database: 383
Effective search space:   149753
Effective search space used:   149753
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: 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