GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Acidovorax sp. GW101-3H11

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 Ac3H11_3016 Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_3016
          Length = 675

 Score =  367 bits (941), Expect = e-106
 Identities = 206/511 (40%), Positives = 303/511 (59%), Gaps = 21/511 (4%)

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

Query: 64  NIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKLDGKR 123
             E II+AA+     AIHPGYGFLSEN +FA+A   AG+ FIGP +  ++ +  K + K+
Sbjct: 62  RWERIIEAAKATGAQAIHPGYGFLSENEDFAQACAAAGLVFIGPPASAIKDMGLKAESKQ 121

Query: 124 LANMAGVPTAPGSDGPVTSIDEAL--KLAEKIGYPIMVKAASGGGGVGITRVDNQDQLMD 181
           L   AGVP  PG  G  +  D AL  + A++IGYP+++KA++GGGG G+  VD  +    
Sbjct: 122 LMEKAGVPLVPGYHG--SDQDPALLQREADRIGYPVLIKASAGGGGKGMRAVDKSEDFAA 179

Query: 182 VWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQKLI 241
             E  KR A  +FG   + +EKY   PRHIE Q+ GD +GN V  +ER+C++QRR+QK++
Sbjct: 180 ALESCKREAINSFGDDAVLVEKYVQRPRHIEIQVFGDMHGNCVYLFERDCSVQRRHQKVL 239

Query: 242 EEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDV-------SRDFYFLELNK 294
           EEAP+P +    R  M E  +   K +NY   GT E                FYF+E+N 
Sbjct: 240 EEAPAPGMTPALRAQMGEAAVAAAKAVNYVGAGTVEFIVEQPGGYERPDQMKFYFMEMNT 299

Query: 295 RLQVEHPTTELIFRIDLVKLQIKLAAGEHLPFSQEDLNKRVRGTAIEYRINAEDALNNFT 354
           RLQVEHP TE I  +DLV+ Q+++A+GE LP  Q+DL  R+ G AIE RI AE+  NNF 
Sbjct: 300 RLQVEHPVTEAITGLDLVEWQLRVASGEPLPLQQQDL--RITGHAIEARICAENPDNNFL 357

Query: 355 GSSGFVTYYREP-----TGPGVRVDSGIESGSYVPPYYDSLVSKLIVYGESREYAIQAGI 409
            ++G +  Y  P         +RVDSG+  G  + P+YDS+V+KLIV+G++RE A+    
Sbjct: 358 PATGALNVYALPECVTFERGAIRVDSGVRQGDAISPFYDSMVAKLIVHGDTREQALARLD 417

Query: 410 RALADYKIGGIKTTIELYKWIMQDPDFQEGKFSTSYISQKTDQFVKYLREQEEIKAAIAA 469
            ALA   I G+ T ++  + + +   F + K  T+ I +  +Q V + +E   +  A AA
Sbjct: 418 DALAQTHIVGLATNVQFLRRVAKTDAFAQAKLDTALIPR--EQAVLFHQEPVGLPLAAAA 475

Query: 470 EIQSRGLLRTSSTDNKGKAQSKSGWKTYGII 500
            + ++ LL+  +++       + G+ T+G++
Sbjct: 476 AV-AQTLLKERASEGVDPFSRRDGFHTHGVV 505


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: 785
Number of extensions: 39
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: 675
Length adjustment: 37
Effective length of query: 472
Effective length of database: 638
Effective search space:   301136
Effective search space used:   301136
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