GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Shewanella halifaxensis HAW-EB4

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate WP_012277981.1 SHAL_RS15030 ATP-grasp domain-containing protein

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



>NCBI__GCF_000019185.1:WP_012277981.1
          Length = 702

 Score =  487 bits (1253), Expect = e-142
 Identities = 281/686 (40%), Positives = 406/686 (59%), Gaps = 45/686 (6%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60
           MF K+LIANRGEIACR+I TA+ MG++TVA+YSDAD +A HV+MADEA ++G      SY
Sbjct: 1   MFTKLLIANRGEIACRIINTAKVMGVRTVALYSDADIDARHVAMADEAFYLGGSAPADSY 60

Query: 61  IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120
           +  + I+E  K +GAEA+HPGYGFLSE  DFA   E A + F+GP + AI++MG K  +K
Sbjct: 61  LKGELIIEIAKRAGAEAIHPGYGFLSENADFALKCEQANIAFVGPSAAAIDSMGSKSAAK 120

Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180
           ++   A V  VPGY G   + +  V  +N++G+P++IKA+ GGGGKGMRI  S  EV + 
Sbjct: 121 EIMGAANVPLVPGYHGDAQNDELLVSEANKMGFPLLIKAAFGGGGKGMRIVESNNEVLDA 180

Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240
             S++ EA +SFG+D++ +E+++ QPRH+E+QV AD HGNC+YL +R+CSIQRR+QKV+E
Sbjct: 181 IHSARREAISSFGNDKLLMERYLRQPRHVEVQVFADSHGNCIYLSDRDCSIQRRHQKVVE 240

Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300
           EAP+P L +A R  MGE A A AKA+ Y  AGTVEF++D   +FYF+EMNTRLQVEHPVT
Sbjct: 241 EAPAPGLSDALRVKMGEAAVAAAKAINYEGAGTVEFLLDTDDSFYFMEMNTRLQVEHPVT 300

Query: 301 ELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRP 360
           EL+TG DLV+  + VA+G  LP +Q++++I G A E+R+YAEDP+ +FLP+ G+L   R 
Sbjct: 301 ELVTGQDLVKWQLMVASGSPLPLKQNEVRIVGHAFEARIYAEDPHNDFLPASGKLDFLRE 360

Query: 361 PVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGI 420
           P +S      VR D+GV E   IS +YDPMI+KL TW  +R  A++ +  ALD +++ G+
Sbjct: 361 PEQS----QFVRIDSGVRENDVISNFYDPMISKLITWDESRPRALQRLVHALDDYQISGL 416

Query: 421 GHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLD-EPTLRR-VAAAAAAMNRVA 478
            HN+ F+  +  H  F   + +T FI E Y D    A  +  P+ RR  A A AA+ ++ 
Sbjct: 417 KHNIEFLANIAKHQAFSDANFSTDFI-ERYGDALLTAQSNATPSTRRDTALAIAALYQLC 475

Query: 479 EIRRTRISGTMNNHERHVGVDWVVALQ---GESYHVSIAADREGSTVSFSDGSSLRVTSD 535
             ++   + T+ +H+ +     V   +      + V++  D         + + L +   
Sbjct: 476 ARKKQAKNDTLTSHDPYSPWGKVSGFRLNSASQHQVALLDDNH-------EINHLELIET 528

Query: 536 WTPGQPLASLMVDGRPLVM----------------KVGKIPM-------GFRLRLR---- 568
              G+P   L +    L +                K+G           G +++L     
Sbjct: 529 QVAGKPQYQLQLSDNLLTLSGELIDEILHAEIVQHKLGDSQAEQASKANGHKIKLPVSQV 588

Query: 569 GADLKVNVRTPRQAELALLMPEKLPPDT-SKYLLCPMPGLVVKINVAEGDEVQEGQALAT 627
           G D  + + +      AL   E    D     L  PM G +V   V+ GD V+ GQ +  
Sbjct: 589 GNDFTLFINSKSYHYRALESEEIEEQDNLEDKLKAPMNGTIVTQLVSVGDVVKAGQGIMV 648

Query: 628 VEAMKMENILRAERRGTVKKIAAAPG 653
           +EAMKME  + +   G V      PG
Sbjct: 649 MEAMKMEYTIESPFDGVVSAFFFEPG 674


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: 1018
Number of extensions: 39
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 666
Length of database: 702
Length adjustment: 39
Effective length of query: 627
Effective length of database: 663
Effective search space:   415701
Effective search space used:   415701
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 24 2021. The underlying query database was built on Sep 17 2021.

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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