Alignments for a candidate for liuB in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for liuB in Burkholderia phytofirmans PsJN

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate BPHYT_RS23275 BPHYT_RS23275 3-methylcrotonyl-CoA carboxylase subunit alpha

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



>FitnessBrowser__BFirm:BPHYT_RS23275
          Length = 692

 Score =  625 bits (1613), Expect = 0.0
 Identities = 356/702 (50%), Positives = 436/702 (62%), Gaps = 61/702 (8%)

Query: 1   MFSKLLIANRGEIACRIIRTARRLGIRTVAVYSDADGDALHVALADEAIRIGGAPAAESY 60
           MF+K+LIANRGEIACR+  T +RLGI +VAVYSDAD +A HVA  DEA+ IGG+ AAESY
Sbjct: 1   MFNKILIANRGEIACRVAATCKRLGIASVAVYSDADANAKHVAACDEAVHIGGSTAAESY 60

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

Query: 121 ALMERSGVPVVPGYHGEEQDASFLADRAREIGYPVLIKARAGGGGKGMRRVERQEDFGPA 180
           ALM  + VP+VPGYHG++QDA  L   A  IGYPVL+KA AGGGGKGMR VER EDF  A
Sbjct: 121 ALMHTAAVPLVPGYHGDDQDAQLLHREADAIGYPVLLKASAGGGGKGMRVVERSEDFEAA 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+ AE++R MGDAAV AA+A+ YVGAGTVEFI   T       FYFMEMNTRLQV
Sbjct: 241 EAPAPGLAAEIKREMGDAAVAAARAVNYVGAGTVEFIMTGTG-----DFYFMEMNTRLQV 295

Query: 301 EHPVTEAITGIDLVEWQLRVASGEPLPKKQADISMNGWAFEARLYAEDPARGFLPATGRL 360
           EHPVTE +TG DLVEWQLRVA+GE LP  Q  + ++G A EAR+YAE PARGFLP+TG L
Sbjct: 296 EHPVTEMVTGQDLVEWQLRVAAGEALPLTQEQLKIDGHAIEARIYAEHPARGFLPSTGTL 355

Query: 361 TELSFPEGTS----------------------RVDSGVRQGDTITPYYDPLIAKLIVHGQ 398
             L  PEG                        R+DSGVR+GDTITP+YDP+IAKLIVHG 
Sbjct: 356 KHLRMPEGVEFTLDAAGSGAAGLGESGRKAPVRIDSGVREGDTITPFYDPMIAKLIVHGA 415

Query: 399 NRSAALGRLQDALKECRIGGTVTNRDFLIRLTEEHDFRSGHPDTGLIDREIERLTAP-VA 457
            R  AL R+  AL  C + G  TN +FL  +     F +G  DTGLI+R  + L AP   
Sbjct: 416 TREEALARMSRALHACEVVGPHTNVEFLQSIVASEPFATGDLDTGLIERHHDALFAPRKK 475

Query: 458 PGDEALALA-AIFSTGALDPNRSTDPWSSLGSWQIWG---------------------DA 495
           P  EALALA A              PW +L  W++ G                     D+
Sbjct: 476 PFKEALALACAALLKREGGTAHGASPWDALSHWRLNGGYTQTLGWRDLESGSAGNAGSDS 535

Query: 496 HRMVVIEHADVRATVTLASRG-RDQFAVRAGASTLPVLVLDRFEGGARLEVAGQKRLIRF 554
                +  A    T TL   G R+ F+   G+       L  +    R  +   +   R 
Sbjct: 536 ESTFTVTFARDGGTQTLEHDGVREDFSWSDGSG------LHEY----RATIGDARATGRV 585

Query: 555 SRDREALTLFHGGRNLVFHVPDGLTGGQSSEIADDELVAPMPGLVKLVRVGAGDAVTKGQ 614
             D +   +F  G  L F   + L     +E  +  L APMPG V  V V  G  V KG 
Sbjct: 586 FVDGDTFHVFCLGEALSFEWQNLLAHAADAEGGEGRLTAPMPGKVIAVLVEPGTVVEKGT 645

Query: 615 ALVVMEAMKMELTLSASREGTIANVHVAEGAQVSEGTVLVTL 656
            L+VMEAMKME T+ A   GT++ V  + G QV++G  L+ L
Sbjct: 646 PLIVMEAMKMEHTIGAPAAGTVSEVLYSVGDQVADGAQLLVL 687


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: 1305
Number of extensions: 74
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 662
Length of database: 692
Length adjustment: 39
Effective length of query: 623
Effective length of database: 653
Effective search space:   406819
Effective search space used:   406819
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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Protein sequences (fasta format)
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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, 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