GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Klebsiella michiganensis M5al

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate BWI76_RS01665 BWI76_RS01665 isocitrate lyase

Query= BRENDA::P9WKK7
         (428 letters)



>FitnessBrowser__Koxy:BWI76_RS01665
          Length = 434

 Score =  513 bits (1320), Expect = e-150
 Identities = 264/427 (61%), Positives = 326/427 (76%), Gaps = 11/427 (2%)

Query: 11  EQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHDLE---WVN 67
           E++ +EW T PRW+ +TR YSAEDVV L+GSV  E TLA+ GA  +W  LH      ++N
Sbjct: 9   EELNKEW-TKPRWEGITRPYSAEDVVKLRGSVNPECTLAQLGAAKMWRLLHGEAKKGYIN 67

Query: 68  ALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNA 127
           +LGALTG  A+QQ +AG++AIYLSGWQVA DANL+   YPDQSLYPANSVP VV RINN 
Sbjct: 68  SLGALTGGQALQQAKAGIEAIYLSGWQVAADANLASSMYPDQSLYPANSVPAVVDRINNT 127

Query: 128 LQRADQI---AKIE-GDTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWED 183
            +RADQI   A IE  D    ++  PIVAD EAGFGG LN +EL K++I AG A  H+ED
Sbjct: 128 FRRADQIQWSAGIELNDPRYTDYFLPIVADAEAGFGGVLNAFELMKSMIEAGAAAVHFED 187

Query: 184 QLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDE 243
           QLAS KKCGH+GGKVL+PTQ+ I+ L +ARLAADV  VPT+VIARTDA+AA LITSD D 
Sbjct: 188 QLASVKKCGHMGGKVLVPTQEAIQKLVAARLAADVMGVPTLVIARTDADAADLITSDCDP 247

Query: 244 RDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKA 303
            D+ FITG+RT EGF+RT  GIE  I+R  AYAP+ADL+W ET TPDLE A++F++A+ A
Sbjct: 248 YDRQFITGDRTSEGFFRTHAGIEQAISRGLAYAPYADLVWCETSTPDLELAKRFADAIHA 307

Query: 304 EYPDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAY 363
           +YP ++LAYNCSPSFNW+K LDD TIA FQ++LA MG+K+QFITLAG H++ ++MFDLA+
Sbjct: 308 KYPGKLLAYNCSPSFNWQKKLDDKTIASFQQQLADMGYKYQFITLAGIHSMWFNMFDLAH 367

Query: 364 GYAQNQ-MSAYVE-LQEREFAAEERGYTATKHQREVGAGYFDRIATTVD-PNSSTTALTG 420
            YAQ + M  YVE +Q+ EFAA + GYT   HQ+EVG GYFD++ T +    SS TALTG
Sbjct: 368 AYAQGEGMKHYVEKVQQPEFAAAKDGYTFVSHQQEVGTGYFDKVTTIIQGGTSSVTALTG 427

Query: 421 STEEGQF 427
           STEE QF
Sbjct: 428 STEESQF 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: 600
Number of extensions: 20
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: 434
Length adjustment: 32
Effective length of query: 396
Effective length of database: 402
Effective search space:   159192
Effective search space used:   159192
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 Sep 17 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