GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Paraburkholderia bryophila 376MFSha3.1

Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate H281DRAFT_01343 H281DRAFT_01343 3-methylcrotonoyl-CoA carboxylase, alpha subunit

Query= metacyc::MONOMER-13597
         (509 letters)



>FitnessBrowser__Burk376:H281DRAFT_01343
          Length = 677

 Score =  348 bits (892), Expect = e-100
 Identities = 191/488 (39%), Positives = 283/488 (57%), Gaps = 19/488 (3%)

Query: 4   FSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSYL 63
           F+++L+ANRGEIA RV    K +G+ ++AVYS+AD  A H    DEA +IG A A +SYL
Sbjct: 2   FNKILIANRGEIACRVAATCKRLGIASVAVYSDADADAKHVSACDEAVHIGGATAAESYL 61

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
            +  II+AA      A+HPGYGFLSEN +FA A E AGI FIGP  E +  +  K   K 
Sbjct: 62  RVARIIEAARATGAQAVHPGYGFLSENEDFAHACEAAGIVFIGPPVEAIAAMGSKAAAKA 121

Query: 124 LANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDVW 183
           L + A VP  PG  G   + +   + A+ IGYP+++KA++GGGG G+  V+  +  +   
Sbjct: 122 LMHAAAVPLVPGYHGDDQNPELLHREADAIGYPVLLKASAGGGGKGMRVVERSEDFLAAL 181

Query: 184 ERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIEE 243
              KR A  +FG   + IEKY   PRH+E Q+  D++G  V  ++R+C++QRR+QK++EE
Sbjct: 182 ASCKREAASSFGNDRVLIEKYLTRPRHVEVQVFADRHGGAVYLFDRDCSVQRRHQKVLEE 241

Query: 244 APSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPTT 303
           AP+P L  + +  M E  +   + +NY   GT E   +  + DFYF+E+N RLQVEHP T
Sbjct: 242 APAPGLSAQIKREMGEAAVAAARAVNYVGAGTVEFIMT-ATGDFYFMEMNTRLQVEHPVT 300

Query: 304 ELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTYY 363
           E+I   DLV+ Q+++AAG+ LP +Q+ L  ++ G AIE RI AE     F  S+G + + 
Sbjct: 301 EMITGQDLVEWQLRVAAGQPLPLTQDQL--KIDGHAIEARIYAEHPARGFLPSTGTLKHL 358

Query: 364 REPTG--------------PGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGI 409
           R P G                VR+DSG+  G  + P+YD +++KLIV+G +RE A+    
Sbjct: 359 RMPEGVEFAIHAGAGESRKAPVRIDSGVREGDTITPFYDPMIAKLIVHGATREEALARMS 418

Query: 410 RALADYKIGGIKTTIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLRE--QEEIKAAI 467
           RAL   ++ G  T +E  + I++   F  G   T  I +  +     +++  +E +  A 
Sbjct: 419 RALHACEVVGPHTNVEFLQRIVESEPFATGDLDTGLIERHHEALFAPVKKPFKEALALAC 478

Query: 468 AAEIQSRG 475
           AA +   G
Sbjct: 479 AALLTREG 486


Lambda     K      H
   0.317    0.135    0.385 

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: 772
Number of extensions: 34
Number of successful extensions: 4
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: 509
Length of database: 677
Length adjustment: 37
Effective length of query: 472
Effective length of database: 640
Effective search space:   302080
Effective search space used:   302080
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 (21.6 bits)
S2: 53 (25.0 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