GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Phyllobacterium brassicacearum STM 196

Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate WP_106713510.1 CU102_RS23445 dihydroxy-acid dehydratase

Query= curated2:P31961
         (608 letters)



>NCBI__GCF_003010955.1:WP_106713510.1
          Length = 578

 Score =  185 bits (469), Expect = 5e-51
 Identities = 165/548 (30%), Positives = 251/548 (45%), Gaps = 47/548 (8%)

Query: 68  VAIVSAYNDMLSAHQPFERFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGME-LSL 126
           VAI++ ++D    H  F+     +K+ + +       AGG P     ++  E  ++  ++
Sbjct: 46  VAILNTWSDAQPCHMHFKDRVEWVKRGVLQ-------AGGFPMELPALSLSENFVKPTTM 98

Query: 127 ASRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTG-I 185
             R+++AM     L  +  D A+ +G CDK  P L++G+L  G LP +F+PAGPM  G  
Sbjct: 99  LYRNMLAMEAEELLRSHPVDGAVLMGGCDKTTPALIMGALSMG-LPFIFLPAGPMLRGNY 157

Query: 186 SNKEKAAVRQLFA------EGKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGL 239
           + K   +    F        G  ++ E    E     + G C   GTA+T   + E MGL
Sbjct: 158 AGKYLGSGTDGFKYWDERRAGTISKVEWQGIEGGIARSYGHCMTMGTASTMTAIAEAMGL 217

Query: 240 HLPGASFVNPNTPLRDELTREAARQASRLTPENGNYVPMAEIVDEKAIVNSVVALLATGG 299
            LPGAS +         ++ +  R+   +  E+   +    IV   A+ N+V   +ATG 
Sbjct: 218 TLPGASSIPAADAGHQRMSTQCGRRIVEMIWED---LTPVRIVTPVAVENAVTVAMATGC 274

Query: 300 STNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLARIYPNGQADI-NHFQAAGGMSFLIR 358
           STN  +H++A+A+ AGI L   D+  +    P +A I P+G + +   F  AGG+  L++
Sbjct: 275 STNAIIHVIAMARRAGIPLELDDLDRIGRTTPVIANIRPSGTSYLMEDFYYAGGLRALMK 334

Query: 359 QLLDGGLLHEDVQTVAGPGLRRYTREPFLEDGRLVWREGPERSLDEAILRPLDKPFSAEG 418
           QL  G  L     TV G  L     E        +W        +E ++RPL  P   EG
Sbjct: 335 QL--GDKLDSSAITVTGTPLTDGLEEV------KIW--------NEDVIRPLTNPVYHEG 378

Query: 419 GLRLMEGNL--GRGVMKVSAVAPEHQVVEAPVRIFHDQASLAAAFKAGE--LERDLVAVV 474
            L +++GNL     V+K +A  P+  + + P  +    A L       +  L  D V V+
Sbjct: 379 SLAVLKGNLCPDGAVIKPAACDPKFHLHKGPALVADSYAELKKIIDDPDYPLTPDTVLVL 438

Query: 475 RFQGPRAN-GMPELHKLTPFLGVLQDRGFK-VALVTDGRMSGASGKVPAAIHVSPEAIAG 532
           R  GP+   GMPE   + P    L   G + +  ++D RMSG S      +H +PEA  G
Sbjct: 439 RNAGPQGGPGMPE-WGMIPMPKALLKLGLRDMMRISDARMSGTSFGA-CVLHAAPEAYVG 496

Query: 533 GPLARLRDGDRVRVDGVNGELRVLVDDAEWQARSLEPAPQDGNLGCGRELFAFMRNAMSS 592
           GPLA LR GD V +D     L +LV D E  AR     P     G G  L       +  
Sbjct: 497 GPLALLRTGDMVEMDIPARSLNMLVTDEELNARRAAWMPPPPRYGRGYGL--MFSKHIEQ 554

Query: 593 AEEGACSF 600
           A++G C F
Sbjct: 555 ADKG-CDF 561


Lambda     K      H
   0.319    0.135    0.397 

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: 831
Number of extensions: 51
Number of successful extensions: 6
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: 608
Length of database: 578
Length adjustment: 37
Effective length of query: 571
Effective length of database: 541
Effective search space:   308911
Effective search space used:   308911
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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