GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Shewanella amazonensis SB2B

Align propionyl-CoA carboxylase α subunit (EC 6.4.1.3) (characterized)
to candidate 6937189 Sama_1359 3-methylcrotonyl-CoA carboxylase alpha subunit (RefSeq)

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



>FitnessBrowser__SB2B:6937189
          Length = 673

 Score =  505 bits (1301), Expect = e-147
 Identities = 292/678 (43%), Positives = 405/678 (59%), Gaps = 30/678 (4%)

Query: 1   MFKKILIANRGEIACRVIKTARKMGIQTVAVYSDADRNALHVSMADEAIHIGPPPANQSY 60
           MF K+LIANRGEIACRVI+TAR MGI+TVAVYSDADR+A HV++ADE+ ++G      SY
Sbjct: 1   MFNKLLIANRGEIACRVIRTARDMGIKTVAVYSDADRDARHVALADESFYLGESAPASSY 60

Query: 61  IVIDKIMEAIKASGAEAVHPGYGFLSERMDFAAALEAAGVVFIGPPSGAIEAMGDKITSK 120
           +  + I++  K  GAEA+HPGYGFLSE   FA A EA+G+ F+GP S AI+AMG K  +K
Sbjct: 61  LRGELIIDIAKKCGAEAIHPGYGFLSENAAFARACEASGIAFVGPGSDAIDAMGSKSAAK 120

Query: 121 KLAKEAGVSTVPGYMGLIADADEAVKISNEIGYPVMIKASAGGGGKGMRIAWSEAEVKEG 180
            + ++AGV  VPGY G        +  + +IGYP++IKA+ GGGGKGMRI  SE+E+K  
Sbjct: 121 LIMEKAGVPLVPGYHGDDQSDATLLAEAKKIGYPLLIKAAYGGGGKGMRIVESESELKAA 180

Query: 181 FESSKNEAANSFGDDRIFIEKFVTQPRHIEIQVLADKHGNCVYLHERECSIQRRNQKVIE 240
            +S++ EAA+SFG+D++ +E+++ QPRH+E+QV AD  GNCVYL +R+CSIQRR+QKV+E
Sbjct: 181 IDSARREAASSFGNDKLLMERYLRQPRHVEVQVFADSQGNCVYLSDRDCSIQRRHQKVVE 240

Query: 241 EAPSPFLDEATRKAMGEQACALAKAVGYASAGTVEFIVDGQKNFYFLEMNTRLQVEHPVT 300
           EAP+P L ++ RK MGE A A AKA+ Y  AGTVEF++D   +F+F+EMNTRLQVEHPVT
Sbjct: 241 EAPAPGLPDSLRKQMGEAAVAAAKAIDYRGAGTVEFLLDVDMSFFFMEMNTRLQVEHPVT 300

Query: 301 ELITGIDLVEQMIRVAAGEKLPFQQSDLKINGWAMESRLYAEDPYRNFLPSIGRLTRYRP 360
           E++TG DLV+  + VAAG +LP +Q +++I+G A E R+YAEDP   FLP+ G+LT  R 
Sbjct: 301 EMVTGQDLVKWQLLVAAGAQLPLEQHEIQIHGHAFEVRIYAEDPNNEFLPASGKLTFLRE 360

Query: 361 PVESVTPTSVVRNDTGVYEGGEISMYYDPMIAKLCTWAPTREAAIEEMRLALDTFEVEGI 420
           P     P+  VR D+GV E   IS YYDPMIAKL  W  +R  A+  +  AL  + V G+
Sbjct: 361 P----EPSRHVRIDSGVRENDVISNYYDPMIAKLIVWDESRPRALARLTRALGDYRVGGL 416

Query: 421 GHNLPFVGAVMDHPRFVKGDITTAFIAEEYPDGFQGAVLDEPTLRRVAAAAAAMNRVAEI 480
            HN+ F+  + +HP F + + +T FI   Y D   G   DE     V A    +      
Sbjct: 417 KHNIEFLSNIAEHPAFAQANFSTDFIG-RYGDALIGDSRDEADTAFVLAVLTQLR----- 470

Query: 481 RRTRISGTMNNHERHVGVDWVVALQGESYHVSIAADREGSTVSFSDGSSLRVTSDWTPGQ 540
            R  +S  +  H+      W  +L+G      +++ R  S     D    R +++ T   
Sbjct: 471 LREAVSQDVAGHDPF--SPW-SSLKG----FRLSSPRRHSVTLLDDAHQSR-SAELTESN 522

Query: 541 PLASLMVDGRPLVMKVGKIPMGFRLRLRGADLKVNVRTPRQAELALL----------MPE 590
               L ++ + + +         +  + G  +KV V          L          + +
Sbjct: 523 GRYQLCLNDKLIELSGSIEDSELKCEINGHKMKVTVSLEDGGLTVFLSSGSYHFREVLGQ 582

Query: 591 KLPPDTSK--YLLCPMPGLVVKINVAEGDEVQEGQALATVEAMKMENILRAERRGTVKKI 648
            L    S    L  PM G VV   VA GD+V  GQ L  +EAMKME  + A   G V + 
Sbjct: 583 VLEETASSEDKLKAPMNGTVVTHLVAAGDKVSAGQGLLVMEAMKMEYTIEAPFDGVVSEF 642

Query: 649 AAAPGASLRVDDVIMEFE 666
             APG  +    +++  E
Sbjct: 643 FFAPGELVSDGTLLLALE 660


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: 1042
Number of extensions: 55
Number of successful extensions: 4
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: 673
Length adjustment: 39
Effective length of query: 627
Effective length of database: 634
Effective search space:   397518
Effective search space used:   397518
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