GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__SB2B:6937189 Sama_1359 3-methylcrotonyl-CoA
           carboxylase alpha subunit (RefSeq)
          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.

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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 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