GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Pedobacter sp. GW460-11-11-14-LB5

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate CA265_RS06590 CA265_RS06590 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-3207
         (400 letters)



>FitnessBrowser__Pedo557:CA265_RS06590
          Length = 391

 Score =  256 bits (655), Expect = 6e-73
 Identities = 161/401 (40%), Positives = 233/401 (58%), Gaps = 11/401 (2%)

Query: 1   MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60
           M++V I  A+RTPIG FGG+LA   A  L    +KA IE    ++ +Q+ EV+ G    A
Sbjct: 1   MKEVVIVSAVRTPIGSFGGSLAQFSATQLGGFAIKAAIE-KAGLKPEQIQEVYMGNVLSA 59

Query: 61  GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120
               +  A  A   AGLP+ +P  T+N++CASG  AI  A ++IA+G+ E+ +AGG+ESM
Sbjct: 60  NL-GQAPATQAAKFAGLPD-LPATTINKVCASGTKAIMLAAQSIANGDNEIIVAGGMESM 117

Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180
           S  P+ + KA +GY    +L    I    +   +   Y    M   A+  A +  ++R  
Sbjct: 118 SNVPYYLDKARNGY----RLGHGQITDGLVKDGLWDVYNDYHMGSAAELCATECNINREA 173

Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGE-TIVERDEHLRPETTLEALTKLKP 239
           QD FA+ S ++A AAQ +G FA EIV + +  +KG+ T+V+ D+        + +  LKP
Sbjct: 174 QDNFAISSYKRAQAAQTSGKFANEIVAIEVKDRKGDITLVDTDDE-PTAVKFDKIPSLKP 232

Query: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPV 299
           V   D TVTA NAS +NDGAAAL+L SA+  K+ GLTP A++LG A    AP      P 
Sbjct: 233 VFKKDGTVTAANASTLNDGAAALVLMSADKAKELGLTPLAKILGYADAQQAPEWFTTAPS 292

Query: 300 PAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLG 359
            A+     +  V ++D D  E+NEAFA   +A  + L + D+  QVN NGGA++LGHPLG
Sbjct: 293 KAIPLALHKANVNINDVDFFEINEAFAVVSIANNQLLALNDN--QVNVNGGAVSLGHPLG 350

Query: 360 MSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
            SGAR+V+T L  L ++ G+ G+A +C G G   AL I ++
Sbjct: 351 ASGARIVVTLLSVLAQNDGKIGVAGICNGGGGASALVIGKL 391


Lambda     K      H
   0.318    0.134    0.383 

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: 346
Number of extensions: 10
Number of successful extensions: 4
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: 400
Length of database: 391
Length adjustment: 31
Effective length of query: 369
Effective length of database: 360
Effective search space:   132840
Effective search space used:   132840
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 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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