GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Herbaspirillum seropedicae SmR1

Align phosphogluconate dehydratase (characterized)
to candidate HSERO_RS16705 HSERO_RS16705 dihydroxy-acid dehydratase

Query= CharProtDB::CH_024239
         (603 letters)



>FitnessBrowser__HerbieS:HSERO_RS16705
          Length = 578

 Score =  185 bits (469), Expect = 5e-51
 Identities = 158/528 (29%), Positives = 251/528 (47%), Gaps = 60/528 (11%)

Query: 68  IAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQDGME-LSL 126
           I I  +Y+++   +  +    E ++  + EA       GG P     ++ G+  +   ++
Sbjct: 46  IGICNTYSELTPCNSHFRALAEQVKIGIWEA-------GGFPLEFPVMSLGETLLRPTAM 98

Query: 127 LSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGPMASGLP 186
           L R + +M     +  N  DG + L  CDK  P L M A S   +P + V  GPM SG  
Sbjct: 99  LYRNLASMDVEESIRANPLDGVVLLMGCDKTTPALLMGAASVD-VPTIGVSGGPMLSG-- 155

Query: 187 NKEKVRIRQLYA------------EGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVV 234
              K R R+L +             GK+ +    E+E+  + + G C   GTA+T   +V
Sbjct: 156 ---KYRGRELGSGTGVWQMSEDVRAGKMTQEEFFEAESCMHRSHGHCMTMGTASTMASMV 212

Query: 235 EFMGMQLPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVAL 294
           E +G+ LP ++ +      R+ L   A R++ +M     E + + K++  +   N I   
Sbjct: 213 EALGVGLPHNAAIPAVDARRNVLARNAGRRIVQMV---EEDLVLSKILTRQAFENAIRVN 269

Query: 295 LATGGSTNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVP 354
            A GGSTN  +HL+A+A   GI+++  D+ D+   +P +  L P+G   +  F  AGG+P
Sbjct: 270 AAIGGSTNAVIHLLAIAGRIGIKLDLKDWDDIGQQLPCLLDLQPSGKFLMEDFYYAGGLP 329

Query: 355 VLVRELLKAGLLHEDVNTVAGFGLSRYTLEPWLNNGEL-DWREGAEKSLDSNVIASFEQP 413
            ++R+L    ++ +   T  G  L       W N  +  +W E         VI SF++P
Sbjct: 330 AVIRQL--ESVIDKTALTANGKTL-------WENCQDAPNWNE--------EVIRSFDKP 372

Query: 414 FSHHGGTKVLSGNLG--RAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRD-- 469
           F    G  +L GNL    AV+K SA           AVVFE+  D+    +   LD D  
Sbjct: 373 FKEAAGIAILKGNLAPDGAVIKPSAATPALLKHRGRAVVFENSDDLHKRIDDENLDVDET 432

Query: 470 CVVVVRHQGPKA-NGMPELHKLMPPLGVLLDRCFKIALVTDGRLSG-ASGKVPSAIHVTP 527
           CV+V+++ GPK   GM E   +  P  +L      +  V+D R+SG A G V   +HV+P
Sbjct: 433 CVLVLKNCGPKGYPGMAEAGNMPLPPKILRKGITDMVRVSDARMSGTAYGTV--VLHVSP 490

Query: 528 EAYDGGLLAKVRDGDIIRVNGQTGELTLLVDEAELAAR-----EPHIP 570
           EA  GG LA V++GD I ++ +  +L L V + ELA R     +P +P
Sbjct: 491 EAAAGGPLAVVQNGDFIELDVEARKLHLDVSDEELARRRAQWQKPELP 538


Lambda     K      H
   0.318    0.134    0.392 

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: 792
Number of extensions: 44
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 603
Length of database: 578
Length adjustment: 37
Effective length of query: 566
Effective length of database: 541
Effective search space:   306206
Effective search space used:   306206
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 (21.7 bits)
S2: 53 (25.0 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