GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Alkalihalobacterium alkalinitrilicum DSM 22532

Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate WP_078430190.1 BK574_RS22725 dihydroxy-acid dehydratase

Query= curated2:P31961
         (608 letters)



>NCBI__GCF_002019605.1:WP_078430190.1
          Length = 555

 Score =  249 bits (637), Expect = 2e-70
 Identities = 173/563 (30%), Positives = 290/563 (51%), Gaps = 52/563 (9%)

Query: 26  MVRAAASKGPHRGTLPCGNLAHGVAACGESDKQTLRLMNQANVAIVSAYNDMLSAHQPFE 85
           M++    + PHR  L         A   E D      M++  + + ++Y D++  H    
Sbjct: 5   MIKKGIDRAPHRSLLRA-------AGVKEED------MDKPFIGVCNSYIDIIPGHMHLN 51

Query: 86  RFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGMELSLASRDVIAMSTAIALSHNMF 145
           +F  + K+A+ E G +  F      + DG+  G  GM  SL SR++I  +    ++ + F
Sbjct: 52  KFAEVAKEAIREAGGI-PFEFNTIGVDDGIAMGHIGMRYSLPSREIICDAAETVINAHWF 110

Query: 146 DAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTGISNKEK----AAVRQ---LFA 198
           D    +  CDKI PG+L+ S+R  ++P+VFV  GPM  G +   K    A+V +    FA
Sbjct: 111 DGVFYIPNCDKITPGMLMASVRT-NVPSVFVSGGPMEAGRTKDGKSLSLASVFEGVGAFA 169

Query: 199 EGKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGLHLPGASFVNPNTPLRDELT 258
            G  +REELL  E ++    G+C+   TAN+   L+E++G+ LPG   +   +  R +L 
Sbjct: 170 SGSMSREELLEIEQSACPTCGSCSGMFTANSMNTLMEMLGVALPGNGTLVATSEGRHQLI 229

Query: 259 REAARQASRLTPENGNYVPMAEIVDEKAIVNSVVALLATGGSTNHTLHLLAIAQAAGIQL 318
           ++AA+    L  ++   +   +I+ ++AI ++    +A GGSTN  LH LAIA  A I  
Sbjct: 230 KDAAKHLMTLIEKD---IRPRDIITKEAIDDAFALDMAMGGSTNTVLHTLAIANEAEIDY 286

Query: 319 TWQDMSELSHVVPTLARIYPNGQADINHFQAAGGMSFLIRQLLD-GGLLHEDVQTVAGPG 377
              D+++++  VP L++I P     ++    AGG+S ++++L    G +H +  T++   
Sbjct: 287 NISDINKIAERVPYLSKISPASDYSMDDVHKAGGVSAIMKELCQIEGAIHPERITIS--- 343

Query: 378 LRRYTREPFLEDGRLVWREGPERSL-DEAILRPLDKPFSAEGGLRLMEGNLG--RGVMKV 434
                       G+ +W    +  + ++ ++R  D P+S+ GGL ++ GNL    GV+KV
Sbjct: 344 ------------GKTIWETVKDAEITNDEVIRRKDNPYSSVGGLSVLFGNLAPDGGVIKV 391

Query: 435 SAVAPEHQVVEAPVRIFHDQASLAAAFKAGELERDLVAVVRFQGPRAN-GMPELHKLTPF 493
            AV    +V E    +++ Q         G++    V V+R++GP+   GMPE+  L P 
Sbjct: 392 GAVDASIKVFEGDAIVYNSQEEALEGINNGDVREGHVVVIRYEGPKGGPGMPEM--LAPT 449

Query: 494 LGVL-QDRGFKVALVTDGRMSGASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVDGVNGE 552
             ++ +  G KVAL+TDGR SGAS  +    H+SPEA  GGP+A + +GD++ +D  N  
Sbjct: 450 SSIVGRGLGTKVALITDGRFSGASRGISIG-HISPEAAEGGPIAFVENGDKITLDLTNRT 508

Query: 553 LRVLVDDAEWQARS---LEPAPQ 572
           + + VDD E   R     EP P+
Sbjct: 509 ITLNVDDVELANRKEGWKEPEPK 531


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: 823
Number of extensions: 50
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: 555
Length adjustment: 36
Effective length of query: 572
Effective length of database: 519
Effective search space:   296868
Effective search space used:   296868
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