GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Persephonella marina EX-H1

Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate WP_012676391.1 PERMA_RS02785 dihydroxy-acid dehydratase

Query= curated2:P31961
         (608 letters)



>NCBI__GCF_000021565.1:WP_012676391.1
          Length = 557

 Score =  263 bits (671), Expect = 2e-74
 Identities = 177/552 (32%), Positives = 283/552 (51%), Gaps = 46/552 (8%)

Query: 25  EMVRAAASKGPHRGTLPCGNLAHGVAACGESDKQTLRLMNQANVAIVSAYNDMLSAHQPF 84
           ++V+    + PHR  L          ACG +D+       +  + I ++Y D++  H   
Sbjct: 4   DIVKKGFERAPHRSLL---------RACGLTDED----FKKPFIGIANSYIDIIPGHVHL 50

Query: 85  ERFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGMELSLASRDVIAMSTAIALSHNM 144
             F  ++K+A+ E G V  F   V  + DG+  G  GM  SL SR++IA S    +  + 
Sbjct: 51  REFAQIVKEAVREAGGV-PFEFNVIGVDDGIAMGHSGMHYSLPSRELIADSIETVVEAHK 109

Query: 145 FDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTG-ISNKEKAAVRQLF------ 197
            DA +C+  CDKIVPG+++ + R  ++P +FV  GPM  G + +     +   F      
Sbjct: 110 LDALVCIPNCDKIVPGMIMAAARL-NIPVIFVSGGPMAAGHLPDGRPIDLATAFEAVGAV 168

Query: 198 AEGKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGLHLPGASFVNPNTPLRDEL 257
           + G  T  EL   E  +  + G+C+   TAN+   L EV+G+ LPG   +    P R EL
Sbjct: 169 SRGLMTENELRVIEENACPSCGSCSGMFTANSMNCLSEVLGIALPGNGSILATDPRRQEL 228

Query: 258 TREAARQASRLTPENGNYVPMAEIVDEKAIVNSVVALLATGGSTNHTLHLLAIAQAAGIQ 317
            R+A  Q  +L   +   +   +IV+E+ I N+    +A GGS+N  LHLLAIA  AGI 
Sbjct: 229 ARKAGEQIVKLVEAD---LKFRDIVNEETIENAFTLDIAMGGSSNTVLHLLAIANEAGID 285

Query: 318 LTWQDMSELSHVVPTLARIYPNGQADINHFQAAGGMSFLIRQLLDGGLLHEDVQTVAGPG 377
              + + ++S   PTL ++ P  Q  +     AGG+S ++++L   GLLH D  TV+   
Sbjct: 286 FPVEKIDQISRRTPTLCKLAPASQYHMEDLDRAGGISAILKELSKKGLLHLDRPTVS--- 342

Query: 378 LRRYTREPFLEDGRLVWREGPERSLDEAILRPLDKPFSAEGGLRLMEGNLG--RGVMKVS 435
               T    +ED  +          D  ++RP+  P+S  GGL ++ GN+    GV+K +
Sbjct: 343 --LKTLGEVIEDAEI---------KDPDVIRPIHNPYSETGGLAVLFGNIAPYGGVVKAA 391

Query: 436 AVAPEHQVVEAPVRIFHDQASLAAAFKAGELERDLVAVVRFQGPRAN-GMPELHKLTPFL 494
           AV P+  V       F  +    A    G+++   V V+R++GPR   GM E+  L+P  
Sbjct: 392 AVDPKIMVHRGKAVCFDSEEEAIAGITGGKVKAGDVVVIRYEGPRGGPGMREM--LSPTS 449

Query: 495 GVL-QDRGFKVALVTDGRMSGASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVDGVNGEL 553
            ++    G KV+L+TDGR SGA+ +     H+SPEA AGGP+  ++DGD + +D  N ++
Sbjct: 450 AIMGMGLGDKVSLITDGRFSGAT-RGACIGHISPEAAAGGPIGIIKDGDEILIDIPNRKI 508

Query: 554 RVLVDDAEWQAR 565
            +L+ + E++ R
Sbjct: 509 ELLISEEEFKKR 520


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: 785
Number of extensions: 49
Number of successful extensions: 8
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: 557
Length adjustment: 36
Effective length of query: 572
Effective length of database: 521
Effective search space:   298012
Effective search space used:   298012
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 Apr 09 2024. 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