GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pimB in Klebsiella michiganensis M5al

Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate BWI76_RS13135 BWI76_RS13135 3-oxoadipyl-CoA thiolase

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



>lcl|FitnessBrowser__Koxy:BWI76_RS13135 BWI76_RS13135
           3-oxoadipyl-CoA thiolase
          Length = 401

 Score =  258 bits (659), Expect = 2e-73
 Identities = 171/413 (41%), Positives = 233/413 (56%), Gaps = 31/413 (7%)

Query: 1   MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKR-AGIDPKEVEDVVMGAAMQ 59
           M +A I    RTPIG+ Y GAL +     L    +   + R    DP  ++DV++G A Q
Sbjct: 1   MRDAFICDGIRTPIGR-YGGALASMRADDLAAIPLRELLSRNPKFDPASIDDVILGCANQ 59

Query: 60  QGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGES 119
            G    N+A  A L AG P T  GTT++R C SGL AI  AAR++     ++ + GG ES
Sbjct: 60  AGEDNRNVAHMATLLAGYPHTVPGTTVNRLCGSGLDAIGFAARAIKAGEADLMIAGGVES 119

Query: 120 ISLV-------------QNDKMNT---FHAVDPALEAIKGDVYMAMLDTAETVAKRYGIS 163
           +S               Q +  +T   +  V+P ++   G    +M +TAE VA+   IS
Sbjct: 120 MSRAPFVMGKASAAYQRQAELFDTTIGWRFVNPLMQQRFGTD--SMPETAENVAELLNIS 177

Query: 164 RERQDEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRP 223
           R  QD ++  SQ+R+A AQ+ G    EI P+    G      GAVS    T+ +DE PR 
Sbjct: 178 RADQDAFAYRSQQRSARAQRDGILAQEIVPVPIIGG-----KGAVS----TVYEDEHPRA 228

Query: 224 ETTAEGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSY 283
           ETT E L+ LK    +G  +TAGNAS ++DGA+A +I S + A A+GL P      M + 
Sbjct: 229 ETTLEQLSRLKTPFRKGGVVTAGNASGVNDGAAALIIASSQQAIAQGLTPRARIVAMATA 288

Query: 284 GCEPDEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGI--DPEKLNV 341
           G EP  MG+GPV AV ++L+R GLS+ D+ L ELNEAFA Q L    +LG+  D   +N 
Sbjct: 289 GVEPKLMGLGPVPAVRKVLERAGLSIKDMDLIELNEAFAAQALGVLRQLGLADDAPHVNP 348

Query: 342 NGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394
           NGGAI++GHP GMSGARLA  A +E +RR  +YA+ TMC+G G G A + E V
Sbjct: 349 NGGAIALGHPLGMSGARLALSASLELQRRSGRYALCTMCIGVGQGIAMILERV 401


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: 405
Number of extensions: 27
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: 395
Length of database: 401
Length adjustment: 31
Effective length of query: 364
Effective length of database: 370
Effective search space:   134680
Effective search space used:   134680
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.

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