GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaJ1 in Klebsiella michiganensis M5al

Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate BWI76_RS16135 BWI76_RS16135 acetyl-CoA acetyltransferase

Query= uniprot:D8ITH5
         (401 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS16135 BWI76_RS16135 acetyl-CoA
           acetyltransferase
          Length = 400

 Score =  617 bits (1590), Expect = 0.0
 Identities = 310/399 (77%), Positives = 352/399 (88%), Gaps = 1/399 (0%)

Query: 2   EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61
           +A ICDA+RTPFGR+GG L  +RADDLAA P+++L+ERNPG+D +R++D++YGCANQAGE
Sbjct: 3   QAFICDAVRTPFGRFGGTLATLRADDLAALPLKALLERNPGLDPARIDDVIYGCANQAGE 62

Query: 62  DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121
           DNRNVARMA LLAGLP +VPGSTVNRLCGSSLDA+G+AARAIKSGE QLMIAGGVESM+R
Sbjct: 63  DNRNVARMALLLAGLPESVPGSTVNRLCGSSLDAIGIAARAIKSGETQLMIAGGVESMSR 122

Query: 122 APFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQD 181
           APFVMGKAESAF+R+  + DTTIGWRF+NP MKA YG+DSMPETAENVA DF I+RADQD
Sbjct: 123 APFVMGKAESAFSRTMRMEDTTIGWRFINPQMKALYGVDSMPETAENVADDFAISRADQD 182

Query: 182 AFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVV 241
           AFALRSQ R AAAQ AG FA E+  +++PQ+KG+PL+ + DEHPR  TT   LA+L+GVV
Sbjct: 183 AFALRSQLRTAAAQEAGRFADELIAVSVPQRKGEPLLFSRDEHPR-TTTAEALARLRGVV 241

Query: 242 RPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPA 301
           RPDGTVTAGNASGVNDGACALLLAS +A     L+P ARV+G+ATAGVAPRIMGFGPAPA
Sbjct: 242 RPDGTVTAGNASGVNDGACALLLASEQALAANDLQPLARVVGVATAGVAPRIMGFGPAPA 301

Query: 302 VRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGAS 361
           VRKVLAQ GLTL QMDVIELNEAFAAQ LAV RDLGLPDDAA+VNPNGGAIA+GHPLGAS
Sbjct: 302 VRKVLAQTGLTLGQMDVIELNEAFAAQALAVTRDLGLPDDAAYVNPNGGAIALGHPLGAS 361

Query: 362 GARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400
           G RL  TA  QL R+GGRYALCTMCIGVGQGIAL+IERV
Sbjct: 362 GGRLAMTAAYQLRRTGGRYALCTMCIGVGQGIALIIERV 400


Lambda     K      H
   0.320    0.135    0.394 

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: 594
Number of extensions: 16
Number of successful extensions: 2
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: 400
Length adjustment: 31
Effective length of query: 370
Effective length of database: 369
Effective search space:   136530
Effective search space used:   136530
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.

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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