GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccA1 in Pseudomonas fluorescens FW300-N2C3

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 AO356_01595 AO356_01595 3-methylcrotonyl-CoA carboxylase

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



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_01595 AO356_01595
           3-methylcrotonyl-CoA carboxylase
          Length = 649

 Score =  363 bits (931), Expect = e-104
 Identities = 193/454 (42%), Positives = 280/454 (61%), Gaps = 4/454 (0%)

Query: 2   PPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPALDS 61
           P  + +LVANRGEIA RV++  + MG+T +AV+S  D+ A H++ AD    +G + A DS
Sbjct: 4   PALTTLLVANRGEIACRVMRTARAMGLTTVAVHSATDRDARHSREADIRVDLGGSKAADS 63

Query: 62  YLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDG 121
           YL I+ +I AA+ +   AIHPGYGFLSENA FA A+E AG+ F+GP +  +  +  K   
Sbjct: 64  YLQIDKLIAAAKASGAQAIHPGYGFLSENAGFARAIENAGLIFLGPPASAIDAMGSKSAA 123

Query: 122 KRLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMD 181
           K L   AGVP  PG  G    ++     AE+IGYP+++KA +GGGG G+  V++  QL +
Sbjct: 124 KTLMETAGVPLVPGYHGEAQDLETFRDAAERIGYPVLLKATAGGGGKGMKVVEDVSQLAE 183

Query: 182 VWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLI 241
                +R A  +FG + + +EKY + PRH+E Q+  D++GN +   ER+C+IQRR+QK++
Sbjct: 184 ALASAQREAQSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVV 243

Query: 242 EEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVEHP 301
           EEAP+P L  + R +M E  ++  + I Y   GT E    D   +F+F+E+N RLQVEHP
Sbjct: 244 EEAPAPGLTPQLRRAMGEAAVRAAQAIGYVGAGTVEFLL-DARGEFFFMEMNTRLQVEHP 302

Query: 302 TTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFTGSSGFVT 361
            TE I  +DLV  QI++A GE LP +Q  +   + G AIE R+ AED  N+F  ++G + 
Sbjct: 303 VTEAITGLDLVAWQIRVAQGEPLPITQAQV--PLLGHAIEVRLYAEDPGNDFLPATGRLA 360

Query: 362 YYREPT-GPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALADYKIGGI 420
            YRE   GPG RVDSG+E G  + P+YD ++ KLI +GE RE A    +  L ++ IGG+
Sbjct: 361 LYRESAEGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFVIGGL 420

Query: 421 KTTIELYKWIMQDPDFQEGKFSTSYISQKTDQFV 454
           KT I   + I+  P F   +  T +I +   Q +
Sbjct: 421 KTNIGFLRRIVAHPAFAAAELDTGFIPRYQAQLL 454


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: 725
Number of extensions: 29
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: 649
Length adjustment: 36
Effective length of query: 473
Effective length of database: 613
Effective search space:   289949
Effective search space used:   289949
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 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