Aligments for a candidate for pccA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments 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:

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