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

GapMind for catabolism of small carbon sources

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

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate H281DRAFT_01343 H281DRAFT_01343 3-methylcrotonoyl-CoA carboxylase, alpha subunit

Query= reanno::Smeli:SM_b21124
         (662 letters)



>FitnessBrowser__Burk376:H281DRAFT_01343
          Length = 677

 Score =  645 bits (1663), Expect = 0.0
 Identities = 363/689 (52%), Positives = 444/689 (64%), Gaps = 48/689 (6%)

Query: 1   MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60
           MF+K+LIANRGEIACR+  T +RLGI +VAVYSDAD DA HV+  DEA+ IGGA AAESY
Sbjct: 1   MFNKILIANRGEIACRVAATCKRLGIASVAVYSDADADAKHVSACDEAVHIGGATAAESY 60

Query: 61  LASAPIVQAARSVGAQAIHPGYGFLSENADFAEAVAEAGMIFVGPPPAAIRAMGLKDAAK 120
           L  A I++AAR+ GAQA+HPGYGFLSEN DFA A   AG++F+GPP  AI AMG K AAK
Sbjct: 61  LRVARIIEAARATGAQAVHPGYGFLSENEDFAHACEAAGIVFIGPPVEAIAAMGSKAAAK 120

Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180
           ALM  + VP+VPGYHG++Q+   L   A  IGYPVL+KA AGGGGKGMR VER EDF  A
Sbjct: 121 ALMHAAAVPLVPGYHGDDQNPELLHREADAIGYPVLLKASAGGGGKGMRVVERSEDFLAA 180

Query: 181 LEAARREAESAFGDGSVLLERYLTKPRHIEMQVFGDRHGNIVHLFERDCSLQRRHQKVIE 240
           L + +REA S+FG+  VL+E+YLT+PRH+E+QVF DRHG  V+LF+RDCS+QRRHQKV+E
Sbjct: 181 LASCKREAASSFGNDRVLIEKYLTRPRHVEVQVFADRHGGAVYLFDRDCSVQRRHQKVLE 240

Query: 241 EAPAPGMTAEVRRAMGDAAVRAAQAIGYVGAGTVEFIADVTNGLWPDHFYFMEMNTRLQV 300
           EAPAPG++A+++R MG+AAV AA+A+ YVGAGTVEFI   T       FYFMEMNTRLQV
Sbjct: 241 EAPAPGLSAQIKREMGEAAVAAARAVNYVGAGTVEFIMTATG-----DFYFMEMNTRLQV 295

Query: 301 EHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRL 360
           EHPVTE ITG DLVEWQLRVA+G+PLP  Q  + ++G A EAR+YAE PARGFLP+TG L
Sbjct: 296 EHPVTEMITGQDLVEWQLRVAAGQPLPLTQDQLKIDGHAIEARIYAEHPARGFLPSTGTL 355

Query: 361 TELSFPEGTS---------------RVDSGVRQGDTITPYYDPLIAKLIVHGQNRSAALG 405
             L  PEG                 R+DSGVR+GDTITP+YDP+IAKLIVHG  R  AL 
Sbjct: 356 KHLRMPEGVEFAIHAGAGESRKAPVRIDSGVREGDTITPFYDPMIAKLIVHGATREEALA 415

Query: 406 RLQDALKECRIGGTVTNRDFLIRLTEEHDFRSGHPDTGLIDREIERLTAPV-APGDEALA 464
           R+  AL  C + G  TN +FL R+ E   F +G  DTGLI+R  E L APV  P  EALA
Sbjct: 416 RMSRALHACEVVGPHTNVEFLQRIVESEPFATGDLDTGLIERHHEALFAPVKKPFKEALA 475

Query: 465 LA-AIFSTGALDPNRSTDPWSSLGSWQI---------W------GDAHRMVVIEHADVRA 508
           LA A   T          PW +L  W++         W      G+      +  A   A
Sbjct: 476 LACAALLTREGGTAHGASPWDALSHWRLNSGFTQTLGWLAIESSGETGSPFTVAFARDGA 535

Query: 509 TVTLASRG-RDQFAVRAGASTLPVLVLDRFEGGARLEVAGQKRLIRFSRDREALTLFHGG 567
           T TL   G R+ F+  +GA       L  +    R  +   +   R   D +   +F  G
Sbjct: 536 TQTLEHDGVREAFSWSSGAG------LHEY----RATIGDARATGRVFIDGDTFHVFCLG 585

Query: 568 RNLVFHVPDGLTGGQSSEIADDELVAPMPGLVKLVRVGAGDAVTKGQALVVMEAMKMELT 627
             L F   + L     +E  +  L APMPG V  V V  G  V KG  L+VMEAMKME T
Sbjct: 586 HALAFEWQNLLAHAADAEHGEGRLTAPMPGKVIAVLVEPGAVVEKGTPLIVMEAMKMEHT 645

Query: 628 LSASREGTIANVHVAEGAQVSEGTVLVTL 656
           + A   GT++ V  A G QV++G  L+ L
Sbjct: 646 IGAPAAGTVSEVLYAVGDQVADGAQLLVL 674


Lambda     K      H
   0.319    0.135    0.394 

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: 1249
Number of extensions: 65
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: 662
Length of database: 677
Length adjustment: 39
Effective length of query: 623
Effective length of database: 638
Effective search space:   397474
Effective search space used:   397474
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 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:

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
the source code
instructions for running GapMind on your computer

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