GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Phaeobacter inhibens BS107

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate GFF1016 PGA1_c10330 methylcrotonoyl-CoA carboxylase subunit alpha

Query= metacyc::MONOMER-13589
         (666 letters)



>FitnessBrowser__Phaeo:GFF1016
          Length = 645

 Score =  483 bits (1243), Expect = e-140
 Identities = 305/684 (44%), Positives = 391/684 (57%), Gaps = 61/684 (8%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60
           MF KILIANRGEIACRV++TAR MG++TVAVYSDAD  A HV MADEA+HIG      SY
Sbjct: 1   MFDKILIANRGEIACRVMETARAMGVRTVAVYSDADVTAKHVQMADEAVHIGGSAPADSY 60

Query: 61  IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120
           +  D I+   + SGA+A+HPGYGFLSE   F  A+EAAG+ FIGP + AI  MG K  +K
Sbjct: 61  LKGDVIIRVAQESGAQAIHPGYGFLSENPAFVDAVEAAGLSFIGPSADAIRKMGLKDAAK 120

Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180
            L ++AGV  VPGY G   DA+     + +IGYPV+IKA AGGGGKGMR+  + AE  + 
Sbjct: 121 ALMEKAGVPVVPGYHGANQDAEFLAGEAEKIGYPVLIKAVAGGGGKGMRLVEAPAEFSDA 180

Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240
            +S++ EA  +FG+  + IEK++ QPRHIE+QV  D   + V+L ER+CS+QRR+QKVIE
Sbjct: 181 LKSAQGEATTAFGNPDVLIEKYIQQPRHIEVQVFGD-GTHAVHLFERDCSLQRRHQKVIE 239

Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQ-----KNFYFLEMNTRLQV 295
           EAP+P +    R+AMGE     A+A+GY  AGTVEFIVDG        F+F+EMNTRLQV
Sbjct: 240 EAPAPGMTAEMREAMGEAGVRAAEAIGYKGAGTVEFIVDGSDGLRTDGFWFMEMNTRLQV 299

Query: 296 EHPVTELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRL 355
           EHPVTELITG+DLVE  +RVA+GE LP QQ DL I G A E+RLYAED  + FLP+ G L
Sbjct: 300 EHPVTELITGVDLVEWQLRVASGESLPAQQDDLTITGHAFEARLYAEDVPKGFLPATGTL 359

Query: 356 TRYRPPVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTF 415
           T    P E        R D+GV  G  IS +YDPMI+K+     TR  A+ ++R AL+  
Sbjct: 360 THLSFPAE-------CRADSGVRAGDTISPWYDPMISKVIVHGATRSVALSKLRRALERT 412

Query: 416 EVEGIGHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMN 475
           EV G   NL F+GA+  H  F +G++ T  IA +       AV D P    +AAA  A+ 
Sbjct: 413 EVAGTVTNLAFLGALASHQGFGRGEVDTGLIARDLE--ALTAVGDMPVAHWIAAAQRAL- 469

Query: 476 RVAEIRRTRISGTMNNHERHVGVDWVVALQGESYHVSIAADREGSTVS--FSDGSSLRVT 533
                     SG  +       +   V L      + I  +  G        D SS  VT
Sbjct: 470 ------CLHKSGGDSGFTLWAPLHRAVQLTHGEESLEITVEVLGPQAQRWQLDDSSHEVT 523

Query: 534 SDWT----PGQPLASLM-VDGRPLVM-KVGKI-----PMGFRLRLRGADLKVNVRTPRQA 582
            D T     G PL ++   DGR  V  ++  I     P+  R    G D  V        
Sbjct: 524 FDGTCWRHDGHPLPNVAEADGRLTVFARISSIFDCIDPLD-RAGTAGGDTNV-------- 574

Query: 583 ELALLMPEKLPPDTSKYLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERR 642
                            +  PMPGLV  +    G EV+EG  LA +EAMKME+ L A R 
Sbjct: 575 -----------------IEAPMPGLVKAVFAEAGAEVKEGDRLAILEAMKMEHSLLAARD 617

Query: 643 GTVKKIAAAPGASLRVDDVIMEFE 666
           G V ++ A+ G  +     ++  E
Sbjct: 618 GVVAEVLASAGDQVEAGAALVRLE 641


Lambda     K      H
   0.318    0.134    0.386 

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: 1079
Number of extensions: 39
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 666
Length of database: 645
Length adjustment: 38
Effective length of query: 628
Effective length of database: 607
Effective search space:   381196
Effective search space used:   381196
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: 54 (25.4 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