GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Algiphilus aromaticivorans DG1253

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate WP_043771407.1 U743_RS06375 isocitrate lyase

Query= BRENDA::P9WKK7
         (428 letters)



>NCBI__GCF_000733765.1:WP_043771407.1
          Length = 437

 Score =  500 bits (1287), Expect = e-146
 Identities = 255/429 (59%), Positives = 320/429 (74%), Gaps = 12/429 (2%)

Query: 11  EQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHD---LEWVN 67
           +Q++ +W TNPRWK V R YSA DVV L+GSV  E+TLAR+GAE LW  ++      +VN
Sbjct: 8   KQLENDWATNPRWKGVKRPYSATDVVRLRGSVQPEYTLARQGAEKLWNLVNGGAKKGYVN 67

Query: 68  ALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNA 127
           + GA++   A+QQ +AGL+A+YLSGWQVA D N S   YPDQSLY  +SVP +VRRINN 
Sbjct: 68  SFGAISAGQAMQQAKAGLEAVYLSGWQVAADGNTSETMYPDQSLYAYDSVPAMVRRINNT 127

Query: 128 LQRADQIA---KIEGDTSVEN---WLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHW 181
            QRAD+I      +G+ S ++   +  PIVAD EAGFGG LN +EL K +I  G AG+H+
Sbjct: 128 FQRADEIQWKKLCDGEMSEKDAIDYFLPIVADAEAGFGGVLNGFELMKNMIRNGAAGAHY 187

Query: 182 EDQLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDV 241
           EDQLA+ KKCGH+GGKVL+PT++ I  L +ARLAADV +VPT+V ARTDAEAA LITSD 
Sbjct: 188 EDQLAAVKKCGHMGGKVLVPTKEAIEKLVAARLAADVLNVPTLVFARTDAEAANLITSDH 247

Query: 242 DERDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAV 301
           D  D PF+TG+RT EGFYR KNG+E  I+R  AYAPFAD++W ETGTPDL  A++F++AV
Sbjct: 248 DANDAPFLTGDRTAEGFYRVKNGLEQAISRGVAYAPFADMVWCETGTPDLGFAKEFADAV 307

Query: 302 KAEYPDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDL 361
           + E P Q+LAYNCSPSFNWKK+LDD TIAKFQ+EL++ G+K+QFITLAG H   Y+ F+ 
Sbjct: 308 RKENPGQLLAYNCSPSFNWKKNLDDKTIAKFQEELSSYGYKYQFITLAGIHINWYNTFEF 367

Query: 362 AYGYAQNQ-MSAYVEL-QEREFAAEERGYTATKHQREVGAGYFDRIATTVDPN-SSTTAL 418
           A+ YAQ + M  Y E+ Q+ EF A E+GYT   HQ+EVGAGYFD + T +    SS TAL
Sbjct: 368 AHKYAQGEGMKHYTEMVQQPEFEAREKGYTFVSHQQEVGAGYFDDVTTVIQGGASSVTAL 427

Query: 419 TGSTEEGQF 427
           TGSTEE QF
Sbjct: 428 TGSTEEEQF 436


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: 588
Number of extensions: 23
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: 437
Length adjustment: 32
Effective length of query: 396
Effective length of database: 405
Effective search space:   160380
Effective search space used:   160380
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 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