GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA in Pseudomonas simiae WCS417

Align Propionyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.3) (characterized)
to candidate GFF3328 PS417_17030 3-methylcrotonyl-CoA carboxylase

Query= reanno::Dino:3607308
         (681 letters)



>FitnessBrowser__WCS417:GFF3328
          Length = 641

 Score =  462 bits (1188), Expect = e-134
 Identities = 276/656 (42%), Positives = 371/656 (56%), Gaps = 40/656 (6%)

Query: 5   ILIANRGEIACRVIKTARKMGIQTVAIYSDADRNALHVRMADEAVHIGPSPANQSYIVID 64
           +L+ANRGEIACRV++TA+ MG+ TVA++S  DR+A H R AD  V +G S A  SY+ ID
Sbjct: 7   LLVANRGEIACRVMRTAKAMGLTTVAVHSAIDRDARHSREADIRVDLGGSKATDSYLQID 66

Query: 65  KVMDAIRQTGAEAVHPGYGFLSENKLFAEALEKEGVAFIGPPANAIEAMGDKITSKKIAQ 124
           K++ A + +GA+A+HPGYGFLSEN  FA A+E  G+ F+GPPA+AI+AMG K  +K + +
Sbjct: 67  KLIAAAQASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKALME 126

Query: 125 EANVSTVPGYMGLIADADEAVKISGEIGYPVMIKASAGGGGKGMRIAWNDAEAREGFQSS 184
            A V  VPGY G   D +        IGYPV++KA+AGGGGKGM++  + ++  E   S+
Sbjct: 127 TAGVPLVPGYHGEAQDLETFRAACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 186

Query: 185 KNEAANSFGDDRIFIEKFVTQPRHIEIQVLADTHGNCIYLGERECSIQRRNQKVVEEAPS 244
           + EA +SFG+ ++ +EK++ +PRH+EIQV AD HG+C+YL ER+CSIQRR+QKVVEEAP+
Sbjct: 187 QREALSSFGNGQMLVEKYLLKPRHVEIQVFADQHGHCLYLNERDCSIQRRHQKVVEEAPA 246

Query: 245 PFLDEATRKAMGEQSCALAQAVGYASAGTVEFIVDGDRNFYFLEMNTRLQVEHPVTELIT 304
           P L    RKAMGE +   AQA+GY  AGTVEF++D    F+F+EMNTRLQVEHPVTE IT
Sbjct: 247 PGLSGEQRKAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEAIT 306

Query: 305 GVDLVEQMIRVAAGEKLPMTQDDVTLTGWAIENRLYAEDPYRNFLPSIGRLTRYRPPVEV 364
           G+DLV   IRVA GE LP+TQ+ V LTG AIE RLYAEDP  +FLP+ GRL  YR   E 
Sbjct: 307 GLDLVAWQIRVAQGEALPITQEQVPLTGHAIEVRLYAEDPTNDFLPATGRLALYR---ES 363

Query: 365 AAGPLEANGKWHGDAPSGPTAVRNDTGVYEGGEISMYYDPMIAKLCTWGPDRPAAIEAMR 424
           A GP                  R D+GV +G  +S +YDPM+ KL  WG DR  A   + 
Sbjct: 364 APGP----------------GRRVDSGVEQGDSVSPFYDPMLGKLIAWGEDREQAQLRLL 407

Query: 425 NALDGFEVEGIGHNLPFVAAVMDHPVFIKGEMTTAFIKEQYPDGFEGVTLGAADLTRLAA 484
             LD F + G+  NL F+  ++ HP F   E+ T FI    P   E +     DL+    
Sbjct: 408 AMLDEFAIGGLKTNLGFLRRIIGHPAFAAAELDTGFI----PRYQEELLPAPGDLSDEFW 463

Query: 485 AAAAMFRVAEIR------------RTRISGTLDNHERMVGTDWVVT-AQDA---RFDVTI 528
            AA    +  +             R  +   +  H    G D +VT A DA   R +  +
Sbjct: 464 QAAGSAFIQSLPPEDGPWGDKRGFRAGLPAEVSLHLSCTGQDRLVTLAADAPPLRGEQLL 523

Query: 529 DADPGGSTVRFADGTAHRVTSRWTPGDSLATVEIDGAPMVLKVDKITSGFRMRFRGADVK 588
               G      A  +   V  RW  G+       D    V        G      G+ V+
Sbjct: 524 IERQGVRRSHLAVRSEGSVFLRW-DGEMHGVTLFDPIAAVEANQSHQGGLTAPMNGSIVR 582

Query: 589 VHVRTPRQAELNDLMPEKLPPDTSKMLLCPMPGLVVKIDVEVGDEVQEGQALCTVE 644
           V V   +  +    +           +  P  G+V  +  + G+ V EG AL  +E
Sbjct: 583 VLVEVGQHVDAGTQLVVLEAMKMEHSIRAPQAGVVKALFCQEGEMVAEGCALVELE 638



 Score = 47.4 bits (111), Expect = 2e-09
 Identities = 25/67 (37%), Positives = 37/67 (55%)

Query: 615 LLCPMPGLVVKIDVEVGDEVQEGQALCTVEAMKMENILRAEKTATVTKINAGAGDSLAVD 674
           L  PM G +V++ VEVG  V  G  L  +EAMKME+ +RA +   V  +    G+ +A  
Sbjct: 572 LTAPMNGSIVRVLVEVGQHVDAGTQLVVLEAMKMEHSIRAPQAGVVKALFCQEGEMVAEG 631

Query: 675 DVIMEFE 681
             ++E E
Sbjct: 632 CALVELE 638


Lambda     K      H
   0.318    0.134    0.392 

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: 1111
Number of extensions: 53
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: 681
Length of database: 641
Length adjustment: 38
Effective length of query: 643
Effective length of database: 603
Effective search space:   387729
Effective search space used:   387729
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:

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