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

GapMind for catabolism of small carbon sources

Aligments 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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources