GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Sinorhizobium meliloti 1021

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate SMc00966 SMc00966 acetyl-COA acyltransferase

Query= metacyc::MONOMER-15952
         (401 letters)



>FitnessBrowser__Smeli:SMc00966
          Length = 397

 Score =  253 bits (645), Expect = 9e-72
 Identities = 171/400 (42%), Positives = 227/400 (56%), Gaps = 35/400 (8%)

Query: 5   LIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYG-CANQAGED 63
           ++I A+RTP+GR  G+LA+V    L A+ ++ +IA    +D + +DDV+ G  AN AG  
Sbjct: 12  VVIAALRTPVGRVNGSLAAVEPARLAALLIERIIA-DTGIDRAEIDDVLVGNAANSAG-- 68

Query: 64  NRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESMSRA 123
             N+AR+AAL AGLPV++PG T++R CGSGL+A+  AAR ++ G     LAGG ES SRA
Sbjct: 69  --NLARLAALEAGLPVAIPGVTVDRQCGSGLEAIVLAARQIQAGAGRFYLAGGTESASRA 126

Query: 124 ------PFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNIS 177
                 P   G+  Q   R+              ++     G   M   AENVA    IS
Sbjct: 127 HIRLRPPLTRGEEPQPVKRA--------------RMAPDSIGDPDMGVAAENVATACGIS 172

Query: 178 RADQDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAK 237
           R  QD FAL S  +A AA A GR ++EIV V   +  GP   +  DE PR + + E L++
Sbjct: 173 RERQDRFALESHRRAVAAEAEGRFSREIVPVPTPE--GP---IARDECPRANASAETLSR 227

Query: 238 LGTPFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGI 297
           L   F  GG+VTAGNA  VNDGA  +L+ +   A++ G +        ATAGVEP+++G+
Sbjct: 228 LRPVFVAGGTVTAGNACPVNDGAAMVLMTNLAEARKLGTRFGLAFTDAATAGVEPKLLGL 287

Query: 298 GPVPATRKV-LELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALG 356
           GPVPA  K+      L +A +D IE NEAFA+Q L  L +L +A   ERVN +GGAIALG
Sbjct: 288 GPVPAMAKLRARNPALDVARVDFIEFNEAFASQVLGSLDQLDIA--PERVNRDGGAIALG 345

Query: 357 HPLGMSGARLVTTALHE-LEERQGRYALCTMCIGVGQGIA 395
           HP G SGA LV     + L        L  M IG G GIA
Sbjct: 346 HPYGASGAILVVRLFSQMLAASSPAEGLAMMGIGGGMGIA 385


Lambda     K      H
   0.319    0.134    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: 428
Number of extensions: 25
Number of successful extensions: 6
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: 397
Length adjustment: 31
Effective length of query: 370
Effective length of database: 366
Effective search space:   135420
Effective search space used:   135420
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