GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garK in Magnetospirillum magneticum AMB-1

Align D-glycerate 2-kinase (EC 2.7.1.-) (characterized)
to candidate WP_050750703.1 AMB_RS11570 glycerate kinase

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



>NCBI__GCF_000009985.1:WP_050750703.1
          Length = 405

 Score =  454 bits (1169), Expect = e-132
 Identities = 245/408 (60%), Positives = 294/408 (72%), Gaps = 5/408 (1%)

Query: 12  LFDSAIEAAHPRHVLADHLPEDRSGRAIVIGAGKAAAAMAEAIEKVWEGELSGLVVTRYE 71
           +F++A+EAA P   L   LP    GR +VIGAGKAAAAMA A+E  W+G LSGLVVTRY 
Sbjct: 1   MFEAAVEAAKPSACLPPALPAPPPGRTLVIGAGKAAAAMARAVEDHWQGPLSGLVVTRYG 60

Query: 72  HHADCKRIEVVEAAHPVPDDAGERVARRVLELVSNLEESDRVIFLLSGGGSSLLALPAEG 131
           H    +RIEVVEAAHPVPD AGE  A R+++L++ +   D V+ L+SGGGS+LLA PAEG
Sbjct: 61  HCVPTRRIEVVEAAHPVPDAAGEHAAGRMMDLLAGVGADDLVLCLISGGGSALLARPAEG 120

Query: 132 ISLADKQAINKALLRSGAHIGEMNCVRKHLSAIKGGRLAKACWPASVYTYAISDVPGDEA 191
           I+LA+KQA+  ALLRSGA IGE+NCVRKHLSA+KGGRLA    PA + T AISDVPGD  
Sbjct: 121 ITLAEKQALTGALLRSGAAIGEINCVRKHLSAVKGGRLAALAAPARLVTLAISDVPGDNP 180

Query: 192 TVIASGPTVADPTTSEQALEILERYHIEVPANVRAWLEDPRSETLKPGDPMLSRSHFRLI 251
           +VIASGPTVADPTT  +A  +L RY I  P  + A L DP +ET K   P      +RLI
Sbjct: 181 SVIASGPTVADPTTLAEARAVLARYGIAPPPAIAARLNDPAAETPKSLPP----GEYRLI 236

Query: 252 ATPQQSLDAAAEVARAAGITPLILGD-LEGEAREVAKVHAGIARQVVLHGQPIAAPCVIL 310
           ATPQ+SL+AAA VA  AG+ PL+LGD LEGEARE+A+V AGI + +  H QP+  P VIL
Sbjct: 237 ATPQRSLEAAALVAARAGLMPLLLGDALEGEAREMARVMAGIVKSIRAHQQPVPMPAVIL 296

Query: 311 SGGETTVTVRGNGRGGRNAEFLLALTENLQGLPNVYALAGDTDGIDGSEDNAGALMMPDS 370
           SGGE TVT+RG G+GG NAEF LAL   L+    V A+A DTDGIDGSEDNAGA++ PD+
Sbjct: 297 SGGEATVTIRGQGKGGPNAEFALALALALKDTQGVEAIACDTDGIDGSEDNAGAVITPDT 356

Query: 371 YARAETLGLRAADALANNDGYGYFAALDDLIVTGPTRTNVNDFRAILI 418
             RA  LGL     L  ND YG+F  L DL+  GPT TNVNDFRA+L+
Sbjct: 357 AERARALGLNLESYLNQNDSYGFFNTLGDLVKCGPTLTNVNDFRAVLV 404


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: 502
Number of extensions: 24
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: 405
Length adjustment: 31
Effective length of query: 392
Effective length of database: 374
Effective search space:   146608
Effective search space used:   146608
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