GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Pandoraea thiooxydans ATSB16

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_047213238.1 PATSB16_RS06380 dihydroxy-acid dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_001931675.1:WP_047213238.1
          Length = 620

 Score =  197 bits (502), Expect = 8e-55
 Identities = 160/542 (29%), Positives = 254/542 (46%), Gaps = 45/542 (8%)

Query: 68  VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127
           +A+V+S+   +  H         + K +   G V +    T A+ DG+  G  GM  SLP
Sbjct: 37  IAVVNSFTQFVPGHVHLRDLGALVAKQIEAAGGVAK-EFNTIAVDDGIAMGHGGMLYSLP 95

Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSG--- 184
           SRE+IA S    ++ +  DA + +  CDKI PG++M A+R  ++P +FV GGPM +G   
Sbjct: 96  SRELIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRL-NIPVVFVSGGPMEAGKVK 154

Query: 185 -------ISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVM 237
                  I+  +  D   + A+ K +  E+ E E  +  + G+C+   TAN+   L E +
Sbjct: 155 SPADGQVIAKIDLIDAMIKAADPKVSDAEIAEVERSACPTCGSCSGMFTANSMNCLTEAI 214

Query: 238 GLHLPGASFVNPYTPLRDALTHEAAQQVTRLTK---QSGNFTPIGEIVDERSLVNSIVAL 294
           GL LPG   +      R  L  +A + V  L +   Q  + + +   +  ++   + ++L
Sbjct: 215 GLALPGNGTIVATHAWRRGLFEQAGRLVVDLCRRYYQEEDASVLPRSIATKAAFENAMSL 274

Query: 295 H-ATGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN-GKADINHFQAAGG 352
             A GGSTN  LH+ A AQ AG+  T  D+  +S  VP L  V P+  K  I     AGG
Sbjct: 275 DVAMGGSTNTVLHLLAAAQEAGVDFTMSDIDRISRRVPCLCKVAPSTDKYHIEDVHRAGG 334

Query: 353 MAFLIRELLEAGLLHEDVNTV----AGRGLSRYTQEPFL-DNGKLVWRDGP--------- 398
           +  ++ EL  A LL     +V     G  ++++       +  +  +R  P         
Sbjct: 335 IMGILGELARAELLDLSCGSVHSGTLGEAIAKWDVAGEAGEEAQKFYRAAPGGIPTTVAF 394

Query: 399 -----IESLDEN----ILRPVARAFSPEGGLRVMEGNLGRG--VMKVSAVALQHQIVEAP 447
                 ++LD +     +R    A+S +GGL V+ GNL     ++K + V     +    
Sbjct: 395 SQEAVFDALDTDRNTGCIRSKQSAYSKDGGLAVLYGNLAEKGCIVKTAGVDESQWVFSGR 454

Query: 448 AVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVAL 506
           A VF+ Q D  +A    ++    V V+R++GP+   GM E+   T +L   +  G   AL
Sbjct: 455 ARVFESQDDAVEAILGDKVVAGDVVVIRYEGPKGGPGMQEMLYPTSYLKS-KGLGKTCAL 513

Query: 507 VTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAARE 566
            TDGR SG S  +    H SPEA  GG +  V +GD+I +D  +  + L V     A+R 
Sbjct: 514 FTDGRFSGGSSGLVIG-HASPEAAEGGTIGLVEEGDVIEIDIPQRKMHLAVSDQVLASRR 572

Query: 567 PA 568
            A
Sbjct: 573 AA 574


Lambda     K      H
   0.318    0.134    0.386 

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: 871
Number of extensions: 43
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: 608
Length of database: 620
Length adjustment: 37
Effective length of query: 571
Effective length of database: 583
Effective search space:   332893
Effective search space used:   332893
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 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