GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Cupriavidus basilensis 4G11

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 RR42_RS29420 RR42_RS29420 3-methylcrotonyl-CoA carboxylase

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



>FitnessBrowser__Cup4G11:RR42_RS29420
          Length = 666

 Score =  360 bits (923), Expect = e-103
 Identities = 200/467 (42%), Positives = 282/467 (60%), Gaps = 5/467 (1%)

Query: 3   PFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDSY 62
           PF ++L+ANRGEIA RV+++   +G   +AVYS AD  A H + A +A YIG+A    SY
Sbjct: 6   PFQKILIANRGEIALRVMRSATALGYRTVAVYSSADAGARHVEEAGQAVYIGQAQPAQSY 65

Query: 63  LNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGK 122
           L I+ II+AA ++  DA+HPGYGFL+ENA FA A  +AG+ FIGPS+E +  + +K   K
Sbjct: 66  LRIDAIIEAARRSGADAVHPGYGFLAENAAFARACREAGLVFIGPSAESIVAMGNKAGAK 125

Query: 123 RLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMDV 182
           RL   A VP  PG  G           AE+IG+P+M+KA +GGGG G+  V +     ++
Sbjct: 126 RLMMAADVPCIPGYQGEDQDEARLCAEAERIGFPVMIKATAGGGGRGMRLVPHARAFPEL 185

Query: 183 WERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLIE 242
               +  A  AFG  ++ +E+  V PRHIE Q++ D+YGN +   ER+C++QRR+QKLIE
Sbjct: 186 LRSARSEAQGAFGDPEVILERAVVEPRHIEIQILADRYGNAIHLGERDCSVQRRHQKLIE 245

Query: 243 EAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHPT 302
           EAPSPA+  E R  M    +   K I Y   GT E    D   ++YF+E+N RLQVEHP 
Sbjct: 246 EAPSPAVSAELRARMGATAVAAVKAIGYEGAGTLEFLL-DRDGNYYFMEMNTRLQVEHPV 304

Query: 303 TELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVTY 362
           TE I  +DLV LQ+++AAGE LP  QED+  R  G AIE R+ AEDA   F   SG +  
Sbjct: 305 TEAITGLDLVALQLRIAAGEPLPLRQEDV--RFSGHAIEVRLCAEDADQGFMPQSGEIAL 362

Query: 363 YREPTGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGIKT 422
           ++ P  P +RV+  + SG+ +PPYYDS+++KLI YG +R+ A +   + L D    G+ T
Sbjct: 363 WQAP--PALRVEHALGSGAAIPPYYDSMIAKLISYGGTRDEARRKLSQGLEDLVALGVTT 420

Query: 423 TIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIKAAIAA 469
                   +  P F  G+ +T++I Q  D  ++      +  AA+AA
Sbjct: 421 NQVFLGRCLAHPAFAAGEATTAFIGQHQDALLQPDAALRQRAAALAA 467


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: 722
Number of extensions: 33
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: 509
Length of database: 666
Length adjustment: 36
Effective length of query: 473
Effective length of database: 630
Effective search space:   297990
Effective search space used:   297990
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