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 GFF3827 PS417_19595 3-methylcrotonyl-CoA carboxylase

Query= reanno::PS:Dsui_0516
         (663 letters)



>FitnessBrowser__WCS417:GFF3827
          Length = 627

 Score =  493 bits (1270), Expect = e-144
 Identities = 287/660 (43%), Positives = 397/660 (60%), Gaps = 38/660 (5%)

Query: 2   FKKILIANRGEIACRVIKTARKMGIKTVAVYSEADKDALFVEMADEAVCIGPAASKESYL 61
           F KILIANRGEIACR+ +TA+ +G +TVAVYS+AD  AL V+MADEAV IGPA  ++SYL
Sbjct: 4   FSKILIANRGEIACRIQRTAQALGYRTVAVYSDADAQALHVQMADEAVHIGPAPVQQSYL 63

Query: 62  VADKIIAACKQTGAEAVHPGYGFLSENAEFSRRLEEEGIKFIGPKHYSIAKMGDKIESKK 121
             D I+ A + T A+A+ PGYGFLSEN +F+R  ++ G+ FIGP   +I  MG K  SK 
Sbjct: 64  NIDAILNAARVTSADAIPPGYGFLSENPDFARACQQAGLTFIGPSPEAIELMGSKRLSKL 123

Query: 122 LAIEAKVNTIPGYNDAIDGPDAAVEIAKKIGYPVMIKASAGGGGKGLRVAYNDAEAHEGF 181
             ++A V  I GY  +          A  IGYP+MIKASAGGGG+G+R+  +  E  +  
Sbjct: 124 AMLDAGVPCIAGYQGSAQDDSTLQREADAIGYPLMIKASAGGGGRGMRLVQHPEELLDNL 183

Query: 182 SSCVNEARNSFGDDRVFIEKYVLEPRHIEIQVLGDSHGNYVYLNERDCSIQRRHQKVIEE 241
            +  +EA+N+FG   + +E+ +++PRH+EIQ+ GDSHG+ +YL ERDCSIQRRHQK+IEE
Sbjct: 184 HTARSEAKNAFGSGELILEQALIDPRHVEIQLFGDSHGHLIYLGERDCSIQRRHQKIIEE 243

Query: 242 APSPFVDPEMRKAMGEQAVALARAVNYESAGTVEFVVSGATKEFYFLEMNTRLQVEHPVT 301
           AP P + PE+R+AMGE A+   RAVNY  AGTVEF++      FYFLEMNTRLQVEHPVT
Sbjct: 244 APCPVMTPELRQAMGEAALNAGRAVNYVGAGTVEFLLD-RNGRFYFLEMNTRLQVEHPVT 302

Query: 302 ELITGLDLVEQMIRVAYGEKLPLTQADVQINGWAMECRINAEDPFRGFLPSTGRLVKFQP 361
           ELITGLDLV+  +++A G+ LPLTQ DV +NG AME R+ AEDP +GFLP TG ++++ P
Sbjct: 303 ELITGLDLVDWQLQIAAGQPLPLTQPDVSLNGHAMEVRLYAEDPAQGFLPQTGEVLRWDP 362

Query: 362 PAEVDGQVRVDTGVYDGGEISMYYDSMIAKLIVHGASREQAIARMRDALNGFVIRGISSN 421
            A     VR+D GV +G  IS +YD M+ K+I +GA+RE+A  ++  A+   V+ G+++N
Sbjct: 363 AA----GVRIDHGVTEGQRISPFYDPMLGKIIAYGATREEARRKLLRAVEDTVLLGVTTN 418

Query: 422 IPFQAALMQHARFQSGIFDTGFIAKEYPKGFDASMVPHDDPALLIGVAAFVHRRYIDRAA 481
            P    L++H  F  G F TGFIA+ +     + + P    A  + +AA +   Y   A 
Sbjct: 419 QPLLVDLLKHPDFVGGDFSTGFIAEHF-----SEIRPLTPSAEHLALAAALF--YQHSAN 471

Query: 482 QVSGQLPGHERKVGDEWVVIRNGERHPVVAKPIEGGYLVTYNGEKYELLSDWRQGQSLFN 541
           Q    L G        W   RN    P   +    G   T N     L +D R    +FN
Sbjct: 472 QHPQGLAG--------W---RNNTSAPCTYRLEVNGDTHTVNAAPLPLTTDGRHANHVFN 520

Query: 542 GTCNGEEFTLQVERHRMTYQLFHWGTRADMMVMSARAAELLALMPEKAAPDLSKFLLSPM 601
           G            R R  Y L         + ++ R  ++ +    + A   S  + +PM
Sbjct: 521 GI-----------RRRTAYHLVGNQLWLPGLTVTDRTQQVAS----RQANVSSGTVKAPM 565

Query: 602 PGLLREVSVAVGQEVKAGEKLAVIEAMKMENILKAEQDCKVKKISVTAGSSLSVDEIIIE 661
            G + +V V+ G  V  G+ L V+EAMKME+ L A  D  +K + V AG  +   ++++E
Sbjct: 566 DGAIVDVRVSAGDSVTKGQLLLVLEAMKMEHPLTAGIDGVIKGVQVIAGDQVRNRQVLLE 625


Lambda     K      H
   0.319    0.135    0.391 

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: 995
Number of extensions: 44
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 663
Length of database: 627
Length adjustment: 38
Effective length of query: 625
Effective length of database: 589
Effective search space:   368125
Effective search space used:   368125
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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