GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadA in Klebsiella michiganensis M5al

Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate BWI76_RS20455 BWI76_RS20455 multifunctional fatty acid oxidation complex subunit alpha

Query= BRENDA::Q64428
         (763 letters)



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

 Score =  520 bits (1339), Expect = e-151
 Identities = 300/717 (41%), Positives = 437/717 (60%), Gaps = 33/717 (4%)

Query: 48  DVAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINML 107
           ++AVI I++P  K+NTL  E  SE   ++ +I  N ++R AV IS+KP  F+AGADINM+
Sbjct: 15  NIAVITIDAPGEKMNTLKAEFASEVRGIIRQIRDNKELRGAVFISAKPDNFIAGADINMI 74

Query: 108 ASCTTPQEAARISQEGQKMFEKLEKSPKPVVAAISGSCLGGGLELAIACQYRIATKDRKT 167
           A C + QEA  ++++GQ++  ++     PV+AAI G+CLGGGLELA+AC  R+ + D KT
Sbjct: 75  ARCHSAQEAEALARQGQQIMAEIHGLSIPVIAAIHGACLGGGLELALACHGRVCSDDDKT 134

Query: 168 VLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLVDPLGP 227
            LG+PEV LG+LPG+GGTQRLP+++GV  A +M+LTG+ +R  +A K GLVD++V     
Sbjct: 135 RLGLPEVQLGLLPGSGGTQRLPRLIGVSGALEMILTGKQLRPRQALKAGLVDEVV----- 189

Query: 228 GIKSPEERTIEYLEEVAVNFA-KGL-ADRKVSAKQSKGLMEKLTSYAMTIPFVRQQVYKT 285
                  +TI  L + AV  A KG  A R V A++            +  P  R  +++ 
Sbjct: 190 ------AQTI--LLQTAVELALKGRPASRAVPARER----------ILAGPLGRSLLFRL 231

Query: 286 VEEKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGELALTKESKALMGLYNG 345
           V +K   +T+G YPA  +I+  ++TGL QG  +GY  E+  FGELA+T +S+AL  ++  
Sbjct: 232 VAKKTHHKTQGNYPATERILQVMETGLAQGCSSGYAEEARAFGELAMTPQSQALRSIFFA 291

Query: 346 QVLCKKNKFGAPQKTV--QQLAILGAGLMGAGIAQVSVDKG-LKTLLKDTTVTGLGRGQQ 402
               KK++ GA  + V  + + ILG GLMG GIA V+  KG L   +KD    G+    +
Sbjct: 292 STDLKKDR-GADAEPVALRSVGILGGGLMGGGIAYVTACKGGLPVRIKDIQPRGINHALK 350

Query: 403 QVFKGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLAVKHKVLKEV 462
             +  L+ +V+++ L + ERD     + G LDY+GF   D+VIEAVFEDLA+K K++ EV
Sbjct: 351 YSWDLLDKQVRRRYLRASERDRQIGLISGSLDYQGFAHRDVVIEAVFEDLALKQKMVSEV 410

Query: 463 ESVTPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQLLEIITTDKTSKDTT 522
           E       IFASNTS+LPI +IAA + RP++VIG+H+FSPVDKM L+E+I    T + T 
Sbjct: 411 EQHCRPETIFASNTSSLPIGEIAAQASRPQRVIGLHFFSPVDKMPLVEVIPHIGTDRQTI 470

Query: 523 ASAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLDALTTGFGFPV 582
           A+AV +   QGK  IVV D  GFY  R LAP ++E +R+L EG   + +D     FGFPV
Sbjct: 471 ATAVKLAKLQGKTPIVVADKAGFYVNRILAPYINEAMRLLMEGEPVEHIDNALVKFGFPV 530

Query: 583 GAATLADEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMVSKGFLGRKSGKGFYIYQSG 642
           G   L DEVGID    +   L  A+GERF      ++  +++    GRK+ +GFY+Y   
Sbjct: 531 GPIQLLDEVGIDTGTKIIPVLEAAWGERF-SPPANIISSILNDDRKGRKNNRGFYLY--A 587

Query: 643 SKNKNLNSEIDNILVNLRLPAKPEVS-SDEDIQYRVITRFVNEAVLCLQEGILATPEEGD 701
           +K +      D  + +L   + P+   S++ +  R +   +NEA  C  E ++ +  +GD
Sbjct: 588 AKGRKSKKRPDPAIYSLLGISSPQARLSEQQVAERCVMMMLNEAARCFDERVVRSARDGD 647

Query: 702 IGAVFGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFTPCQLLRDLANNSS 758
           IGAVFG+GFPP LGGPFR++D  GA +V   L++  + YG +FTPC  L  +A   +
Sbjct: 648 IGAVFGIGFPPFLGGPFRYMDTLGAGEVAAILQRLAAQYGPRFTPCDTLLHMAEQGA 704


Lambda     K      H
   0.317    0.135    0.380 

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: 1070
Number of extensions: 45
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 763
Length of database: 714
Length adjustment: 40
Effective length of query: 723
Effective length of database: 674
Effective search space:   487302
Effective search space used:   487302
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: 55 (25.8 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 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