GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Echinicola vietnamensis KMM 6221, DSM 17526

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate Echvi_3705 Echvi_3705 acetyl-CoA acetyltransferases

Query= SwissProt::P0C7L2
         (401 letters)



>FitnessBrowser__Cola:Echvi_3705
          Length = 393

 Score =  241 bits (616), Expect = 2e-68
 Identities = 144/410 (35%), Positives = 226/410 (55%), Gaps = 27/410 (6%)

Query: 1   MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60
           M+E +I   +RTP+G +GG LS + A +L A  ++  L R  ++  E +D+VI+G    A
Sbjct: 1   MKEVYIISAVRTPLGSFGGKLSGLTAVELGAQAIKGALGR-AQVTPEQVDEVIMGNVLSA 59

Query: 61  GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120
               +  AR A + AG+   V  TT+N++C SG+ ++ FAA++I  G  D+++AGG+ESM
Sbjct: 60  NL-GQAPARQAAIGAGIGYHVPCTTVNKVCASGMKSVMFAAQSIMTGQSDIIVAGGMESM 118

Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPET---------AENVA 171
           S  P+ + KA               G++F N         D + E          A+N A
Sbjct: 119 SNVPYYIPKAR-------------FGYKFGNGEFVDGLAKDGLHEVYYNFPMGNCADNTA 165

Query: 172 ELLKISREDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETT 231
           +   ISRE QD +A++S +R A+A  +    +E++PV  K++KG    +  DE  +    
Sbjct: 166 KEKNISREAQDEYAIQSYRRAAEAWKAQAFQDEVIPVTFKSRKGESITVDEDEEYQ-NVL 224

Query: 232 LEQLRGLKAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVE 291
            E++  L+  F   G +TA NAS +NDGAAAL++ S++ A A GL P A+I+  A A  +
Sbjct: 225 FEKIPSLRPVFDKEGTVTAANASTMNDGAAALVLMSKEKAEALGLQPVAKILGFADAATD 284

Query: 292 PRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGG 351
           P      P  A  + L+ AG+    +D  E+NEAF+A AL   +EL +P+D   +N  GG
Sbjct: 285 PIWFTTAPALAIPKALKNAGIQAEAVDYYEINEAFSAVALANQQELNIPND--RLNVFGG 342

Query: 352 AIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401
           A++LGHPLG SGAR+       L ++ G+  +  +C G G   AM++E +
Sbjct: 343 AVSLGHPLGASGARIMATLHSVLRQKGGKIGVAGICNGGGGASAMVIENL 392


Lambda     K      H
   0.319    0.135    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: 370
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: 401
Length of database: 393
Length adjustment: 31
Effective length of query: 370
Effective length of database: 362
Effective search space:   133940
Effective search space used:   133940
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: 50 (23.9 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