GapMind for catabolism of small carbon sources

 

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

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate Echvi_1071 Echvi_1071 acetyl-CoA acetyltransferases

Query= metacyc::MONOMER-20679
         (395 letters)



>FitnessBrowser__Cola:Echvi_1071
          Length = 391

 Score =  256 bits (653), Expect = 1e-72
 Identities = 154/393 (39%), Positives = 223/393 (56%), Gaps = 5/393 (1%)

Query: 3   EAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRA-GIDPKEVEDVVMGAAMQQG 61
           +A I+   RT +GKA +G         L    I+  +    G++ + V+D+++G A+ + 
Sbjct: 2   DAYIIKGYRTAVGKAKKGGFRFYRPDDLAVDVIKKLIADTPGLEAERVDDLIVGNAVPEA 61

Query: 62  ATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS 121
             G  + R   L A L     G  I+R C SGL+AIALA   +     +  + GG ES+S
Sbjct: 62  EQGMQMGRMISLMA-LGKVVPGFIINRYCGSGLEAIALATAKIKSGMADCIIAGGTESMS 120

Query: 122 LVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAAA 181
           +V      T  A++  + +   D Y++M  TAE +AK Y ISRE  D++++ S  R  +A
Sbjct: 121 MVPMMGYKT--ALNWKIASEHPDYYLSMGLTAEELAKDYDISREDSDQFAVTSHERAISA 178

Query: 182 QQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGEGF 241
            + G+F +EI PI  +   VD A+G    +  T+  DEGPRP T  + L GLK    +G 
Sbjct: 179 IKEGRFKEEIVPIEVEETFVD-ASGKRQTRTFTVDTDEGPRPGTNMDVLGGLKPAFKQGG 237

Query: 242 TITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVPRL 301
            +TAGN+SQ SDGA+ TV+MS++      L+P+         G +P  MGIGP  AVP+ 
Sbjct: 238 QVTAGNSSQTSDGAAFTVVMSERMVKELNLEPVARLVSYSVAGVDPRIMGIGPKEAVPKA 297

Query: 302 LKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARLAG 361
           LK+ G+ + DI L ELNEAFA Q L     L +DP  +NVNGGA+++GHP G +GA+L  
Sbjct: 298 LKQAGMKMSDISLVELNEAFAAQALAVIRALDMDPNTVNVNGGAVALGHPLGCTGAKLTV 357

Query: 362 HALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
             + E RRR  KY +VT CVGGG G AG+ E++
Sbjct: 358 QMINELRRRNQKYGMVTACVGGGQGVAGVVELL 390


Lambda     K      H
   0.316    0.134    0.378 

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: 411
Number of extensions: 16
Number of successful extensions: 3
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: 395
Length of database: 391
Length adjustment: 31
Effective length of query: 364
Effective length of database: 360
Effective search space:   131040
Effective search space used:   131040
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: 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