GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Acidovorax sp. GW101-3H11

Align isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate Ac3H11_2831 Isocitrate lyase (EC 4.1.3.1)

Query= BRENDA::P9WKK7
         (428 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2831
          Length = 443

 Score =  491 bits (1263), Expect = e-143
 Identities = 247/426 (57%), Positives = 314/426 (73%), Gaps = 10/426 (2%)

Query: 13  IQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQLHD---LEWVNAL 69
           ++++W TNPRWK V R YSA DVV L+GS+  EHTLA+RGAE LW++++      +VNA 
Sbjct: 18  LEKDWATNPRWKGVKRGYSAADVVRLRGSLPIEHTLAKRGAEKLWDKINGGAKKGYVNAF 77

Query: 70  GALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQVVRRINNALQ 129
           GA++   A+QQ +AGL+A+YLSGWQVA D N S   YPDQSLY  +SVP +VRRINN  +
Sbjct: 78  GAISAGQAMQQAKAGLEAVYLSGWQVAADGNTSETMYPDQSLYAYDSVPTMVRRINNTFK 137

Query: 130 RADQI----AKIEGDTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSHWEDQL 185
           RAD+I        GD    ++  PIVAD EAGFGG LN +EL K +I +G AG H+EDQL
Sbjct: 138 RADEIQWGRGINPGDKEFIDYFLPIVADAEAGFGGVLNAFELMKNMIQSGAAGVHFEDQL 197

Query: 186 ASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSDVDERD 245
           A+ KKCGH+GGKVL+PTQ+    L SAR AADV  V T+V+ARTDAEAA LITSD D  D
Sbjct: 198 AAVKKCGHMGGKVLVPTQEACEKLISARFAADVMGVSTIVLARTDAEAANLITSDHDAND 257

Query: 246 QPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEAVKAEY 305
           +PF+TGERT+EGFYR KNG+E  I+R  AYAP+ADL+W ETG PD+  AR+F++AV A  
Sbjct: 258 KPFLTGERTQEGFYRVKNGLEQAISRGVAYAPYADLVWCETGVPDIGFAREFAQAVHAAC 317

Query: 306 PDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFDLAYGY 365
           P ++L+YNCSPSFNWKK+L+D  IA FQ++L+A+G+K+QFITLAG H   ++ F  A+ Y
Sbjct: 318 PGKLLSYNCSPSFNWKKNLNDKQIASFQEDLSALGYKYQFITLAGIHINWFNTFQFAHAY 377

Query: 366 AQNQ-MSAYVEL-QEREFAAEERGYTATKHQREVGAGYFDRIATTVDPNSSTT-ALTGST 422
           A  + M  YV + QE EFAA ++GYT   HQ+EVGAGYFD + T +   SS+  ALTGST
Sbjct: 378 ANGEGMKHYVNMVQEPEFAARDKGYTFVSHQQEVGAGYFDDVTTVIQGGSSSVKALTGST 437

Query: 423 EEGQFH 428
           EE QFH
Sbjct: 438 EEEQFH 443


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: 599
Number of extensions: 28
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: 443
Length adjustment: 32
Effective length of query: 396
Effective length of database: 411
Effective search space:   162756
Effective search space used:   162756
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