GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pimF in Klebsiella michiganensis M5al

Align 6-carboxyhex-2-enoyl-CoA hydratase (characterized)
to candidate BWI76_RS20455 BWI76_RS20455 multifunctional fatty acid oxidation complex subunit alpha

Query= metacyc::MONOMER-20678
         (699 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS20455 BWI76_RS20455
           multifunctional fatty acid oxidation complex subunit
           alpha
          Length = 714

 Score =  339 bits (869), Expect = 3e-97
 Identities = 234/708 (33%), Positives = 354/708 (50%), Gaps = 45/708 (6%)

Query: 11  DQVAIVTVDSP--PVNALSAAVR---RGILENVNAAVADPAVQAIVLVCAGR-TFIAGAD 64
           D +A++T+D+P   +N L A      RGI+  +     +  ++  V + A    FIAGAD
Sbjct: 14  DNIAVITIDAPGEKMNTLKAEFASEVRGIIRQIRD---NKELRGAVFISAKPDNFIAGAD 70

Query: 65  ITEFGK---PPQPPAL----NDVIAALENSPKPTIAAIHGTALGGGLEVALGCHFRVAVK 117
           I    +     +  AL      ++A +     P IAAIHG  LGGGLE+AL CH RV   
Sbjct: 71  INMIARCHSAQEAEALARQGQQIMAEIHGLSIPVIAAIHGACLGGGLELALACHGRVCSD 130

Query: 118 EAK--LGLPEVKLGLLPGAGGTQRLPRAVGPELAVQMIVGGSPIGAAEALKHGLVEEVVE 175
           + K  LGLPEV+LGLLPG+GGTQRLPR +G   A++MI+ G  +   +ALK GLV+EVV 
Sbjct: 131 DDKTRLGLPEVQLGLLPGSGGTQRLPRLIGVSGALEMILTGKQLRPRQALKAGLVDEVVA 190

Query: 176 NLVAGAVAFAKKVLAEKRPLRRLRDDDSKLAAAKADRSIFTNAVAAMT--KKARGLEAPF 233
             +   +  A ++  + RP  R      ++ A    RS+    VA  T  K      A  
Sbjct: 191 QTIL--LQTAVELALKGRPASRAVPARERILAGPLGRSLLFRLVAKKTHHKTQGNYPATE 248

Query: 234 ACADAIGAAIDLPFEEGLKKEREGFMKLVVSDQSKAQRYAFFAEREAAKVDGVPDGTKPR 293
                +   +      G  +E   F +L ++ QS+A R  FFA  +  K  G     +P 
Sbjct: 249 RILQVMETGLAQGCSSGYAEEARAFGELAMTPQSQALRSIFFASTDLKKDRGAD--AEPV 306

Query: 294 PVSRVAIIGAGTMGGGIA-MSFANAGIPVTLIETGEEQLKRGLGIMQKNWEATAARGGLP 352
            +  V I+G G MGGGIA ++    G+PV + +     +   L       +    R  L 
Sbjct: 307 ALRSVGILGGGLMGGGIAYVTACKGGLPVRIKDIQPRGINHALKYSWDLLDKQVRRRYLR 366

Query: 353 PDAPAKRMALITGLVGLENVKDADLIIEAVFETMAVKKEVFTAVDAHAKPGAVLASNTSY 412
                +++ LI+G +  +     D++IEAVFE +A+K+++ + V+ H +P  + ASNTS 
Sbjct: 367 ASERDRQIGLISGSLDYQGFAHRDVVIEAVFEDLALKQKMVSEVEQHCRPETIFASNTSS 426

Query: 413 LSIDEIAATTKRPQDVLGMHFFSPANVMKLCEIVRGAKTAPDALLTAVSIAKKIAKVPVV 472
           L I EIAA   RPQ V+G+HFFSP + M L E++    T    + TAV +AK   K P+V
Sbjct: 427 LPIGEIAAQASRPQRVIGLHFFSPVDKMPLVEVIPHIGTDRQTIATAVKLAKLQGKTPIV 486

Query: 473 VGVCDGFVGNRMLAARSKQSEKLLFEGALPQQVDAVVTKFGMPMGPFAMGDLAGLDIG-- 530
           V    GF  NR+LA    ++ +LL EG   + +D  + KFG P+GP  + D  G+D G  
Sbjct: 487 VADKAGFYVNRILAPYINEAMRLLMEGEPVEHIDNALVKFGFPVGPIQLLDEVGIDTGTK 546

Query: 531 --------WRSRKDRGIKSEIADALCEAGRFGQKTGKGYYKYEQGSR--APMPDPEVETL 580
                   W  R      + I  ++    R G+K  +G+Y Y    R     PDP + +L
Sbjct: 547 IIPVLEAAWGERFSP--PANIISSILNDDRKGRKNNRGFYLYAAKGRKSKKRPDPAIYSL 604

Query: 581 INDTLAKLGLKRRDITDEEILERMVYPMINEGARILEEKIAARPSDIDVVWLYGYGWPIY 640
           +      +   +  ++++++ ER V  M+NE AR  +E++     D D+  ++G G+P +
Sbjct: 605 LG-----ISSPQARLSEQQVAERCVMMMLNEAARCFDERVVRSARDGDIGAVFGIGFPPF 659

Query: 641 RGGPMHYADSVGLKHIAERLSAYAKATNDPSLEPAPLLARLAAEGKTF 688
            GGP  Y D++G   +A  L   A A   P   P   L  +A +G TF
Sbjct: 660 LGGPFRYMDTLGAGEVAAILQRLA-AQYGPRFTPCDTLLHMAEQGATF 706


Lambda     K      H
   0.317    0.134    0.383 

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: 1017
Number of extensions: 56
Number of successful extensions: 6
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: 699
Length of database: 714
Length adjustment: 39
Effective length of query: 660
Effective length of database: 675
Effective search space:   445500
Effective search space used:   445500
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 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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