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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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