GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuB in Pseudomonas simiae WCS417

Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate GFF3328 PS417_17030 3-methylcrotonyl-CoA carboxylase

Query= reanno::pseudo1_N1B4:Pf1N1B4_3984
         (651 letters)



>lcl|FitnessBrowser__WCS417:GFF3328 PS417_17030 3-methylcrotonyl-CoA
           carboxylase
          Length = 641

 Score = 1075 bits (2779), Expect = 0.0
 Identities = 548/646 (84%), Positives = 584/646 (90%), Gaps = 9/646 (1%)

Query: 6   LTTLLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYL 65
           LTTLLVANRGEIACRVMRTAKA+GLTTVAVHSA DRDARHSREADIRVDLGGSKA DSYL
Sbjct: 4   LTTLLVANRGEIACRVMRTAKAMGLTTVAVHSAIDRDARHSREADIRVDLGGSKATDSYL 63

Query: 66  QIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKA 125
           QIDKLIAAA+ASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKA
Sbjct: 64  QIDKLIAAAQASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKA 123

Query: 126 LMETAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEAL 185
           LMETAGVPLVPGYHGEAQDLETFR ACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEAL
Sbjct: 124 LMETAGVPLVPGYHGEAQDLETFRAACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEAL 183

Query: 186 ASAQREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEE 245
           ASAQREALSSFG+ +MLVEKYLLKPRHVEIQVFADQHG+CLYLNERDCSIQRRHQKVVEE
Sbjct: 184 ASAQREALSSFGNGQMLVEKYLLKPRHVEIQVFADQHGHCLYLNERDCSIQRRHQKVVEE 243

Query: 246 APAPGLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTE 305
           APAPGLS E R+AMGEAAVR+AQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTE
Sbjct: 244 APAPGLSGEQRKAMGEAAVRAAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTE 303

Query: 306 AITGLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDFLPATGRLALYRES 365
           AITGLDLVAWQIRVA+GEALP+TQ+QVPL GHAIEVRLYAEDP NDFLPATGRLALYRES
Sbjct: 304 AITGLDLVAWQIRVAQGEALPITQEQVPLTGHAIEVRLYAEDPTNDFLPATGRLALYRES 363

Query: 366 AAGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGLKTNIN 425
           A GPGRRVDSGVE+GD +SPFYDPMLGKLIAWGEDREQA+LRLL+MLDEFAIGGLKTN+ 
Sbjct: 364 APGPGRRVDSGVEQGDSVSPFYDPMLGKLIAWGEDREQAQLRLLAMLDEFAIGGLKTNLG 423

Query: 426 FLRRIIGHPAFAAAELDTGFIPRYQEQLLPAPSDLSDEFWQAAAQAFAQSQSSTTRADDL 485
           FLRRIIGHPAFAAAELDTGFIPRYQE+LLPAP DLSDEFWQAA  AF QS          
Sbjct: 424 FLRRIIGHPAFAAAELDTGFIPRYQEELLPAPGDLSDEFWQAAGSAFIQSLPPE------ 477

Query: 486 SSPWGIGNGFRAGLPTEITLHLSCEEQDRALTLGDADAHTAQLKGEYLLTEHNGLRRQHR 545
             PWG   GFRAGLP E++LHLSC  QDR +TL    A    L+GE LL E  G+RR H 
Sbjct: 478 DGPWGDKRGFRAGLPAEVSLHLSCTGQDRLVTLA---ADAPPLRGEQLLIERQGVRRSHL 534

Query: 546 AIRRGDTLYLQWDGELRRIESYDPISAVEASHSHQGGLTAPMNGSIVRVLVEAGQTVEAG 605
           A+R   +++L+WDGE+  +  +DPI+AVEA+ SHQGGLTAPMNGSIVRVLVE GQ V+AG
Sbjct: 535 AVRSEGSVFLRWDGEMHGVTLFDPIAAVEANQSHQGGLTAPMNGSIVRVLVEVGQHVDAG 594

Query: 606 AQLVVLEAMKMEHSIRAPHAGIIKALYCQEGEMVSEGSALVELEHA 651
            QLVVLEAMKMEHSIRAP AG++KAL+CQEGEMV+EG ALVELE A
Sbjct: 595 TQLVVLEAMKMEHSIRAPQAGVVKALFCQEGEMVAEGCALVELEPA 640


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: 1362
Number of extensions: 39
Number of successful extensions: 3
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: 651
Length of database: 641
Length adjustment: 38
Effective length of query: 613
Effective length of database: 603
Effective search space:   369639
Effective search space used:   369639
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