Aligments for a candidate for pccA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments 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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources