GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Sedimenticola selenatireducens DSM 17993

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_029133164.1 A3GO_RS0109300 isocitrate lyase

Query= BRENDA::P9WKK7
         (428 letters)



>NCBI__GCF_000428045.1:WP_029133164.1
          Length = 436

 Score =  521 bits (1342), Expect = e-152
 Identities = 263/427 (61%), Positives = 325/427 (76%), Gaps = 10/427 (2%)

Query: 11  EQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHDLE---WVN 67
           E ++++W  NPRWK V R YSAEDVV L+GSV  E+T A+RGA+ LW+ +H      +VN
Sbjct: 8   EALEKDWAENPRWKTVKRGYSAEDVVRLRGSVQPEYTYAKRGADKLWDLVHGSAKKGYVN 67

Query: 68  ALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNA 127
            +GA+TG  A+QQ +AG++AIYLSGWQVA D N S   YPDQSLY  +SVP +VRRINNA
Sbjct: 68  CMGAITGGQAMQQAKAGIEAIYLSGWQVAADGNTSETMYPDQSLYAYDSVPTMVRRINNA 127

Query: 128 LQRADQIAKIEG----DTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWED 183
            +RAD+I    G    D    ++  PIVAD EAGFGG LN +EL K +IA G AG H+ED
Sbjct: 128 FKRADEIQWSRGTGPEDQGYIDYFLPIVADAEAGFGGVLNAFELMKNMIANGAAGVHFED 187

Query: 184 QLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDE 243
           QLA+ KKCGH+GGKVL+PTQ+ ++ L +ARLAADV  VPT+++ARTDAEAATL+TSD D 
Sbjct: 188 QLAAVKKCGHMGGKVLVPTQEAVQKLIAARLAADVCGVPTLLLARTDAEAATLLTSDFDP 247

Query: 244 RDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKA 303
            D+PF+TGERT EGFY  KNG+E  I+R  AYAP+ADL+W ETGTPDL  AR+F+EAV  
Sbjct: 248 NDKPFVTGERTPEGFYNVKNGLEQAISRGVAYAPYADLVWCETGTPDLGFAREFAEAVLE 307

Query: 304 EYPDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAY 363
           + P ++LAYNCSPSFNWKK+LDDATIAKFQ EL+ MG+K+QFITLAG H + Y+MFDLAY
Sbjct: 308 KNPGKLLAYNCSPSFNWKKNLDDATIAKFQDELSDMGYKYQFITLAGIHNMWYNMFDLAY 367

Query: 364 GYAQNQ-MSAYVE-LQEREFAAEERGYTATKHQREVGAGYFDRIATTVDPN-SSTTALTG 420
            YA+ + M  YVE +QE EFAA ++GYT   HQ+EVG GYFD + TT+    SS TALTG
Sbjct: 368 DYARGEGMKHYVEKVQEPEFAARDKGYTFVSHQQEVGVGYFDDVTTTIQGGASSVTALTG 427

Query: 421 STEEGQF 427
           STEE QF
Sbjct: 428 STEEEQF 434


Lambda     K      H
   0.316    0.130    0.384 

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: 612
Number of extensions: 21
Number of successful extensions: 5
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: 428
Length of database: 436
Length adjustment: 32
Effective length of query: 396
Effective length of database: 404
Effective search space:   159984
Effective search space used:   159984
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 (21.6 bits)
S2: 51 (24.3 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