GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadA in Escherichia coli BW25113

Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate 16447 b2341 fused enoyl-CoA hydratase and epimerase and isomerase/3-hydroxyacyl-CoA dehydrogenase (NCBI)

Query= BRENDA::Q64428
         (763 letters)



>lcl|FitnessBrowser__Keio:16447 b2341 fused enoyl-CoA hydratase and
           epimerase and isomerase/3-hydroxyacyl-CoA dehydrogenase
           (NCBI)
          Length = 714

 Score =  535 bits (1379), Expect = e-156
 Identities = 296/708 (41%), Positives = 436/708 (61%), Gaps = 26/708 (3%)

Query: 48  DVAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINML 107
           ++AVI I+ P  K+NTL  E  S+   ++ ++  N ++R  V +S+KP  F+AGADINM+
Sbjct: 15  NIAVITIDVPGEKMNTLKAEFASQVRAIIKQLRENKELRGVVFVSAKPDNFIAGADINMI 74

Query: 108 ASCTTPQEAARISQEGQKMFEKLEKSPKPVVAAISGSCLGGGLELAIACQYRIATKDRKT 167
            +C T QEA  ++++GQ++  ++   P  V+AAI G+CLGGGLELA+AC  R+ T D KT
Sbjct: 75  GNCKTAQEAEALARQGQQLMAEIHALPIQVIAAIHGACLGGGLELALACHGRVCTDDPKT 134

Query: 168 VLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLVDPLGP 227
           VLG+PEV LG+LPG+GGTQRLP+++GV  A +M+LTG+ +RA +A K+GLVD +V     
Sbjct: 135 VLGLPEVQLGLLPGSGGTQRLPRLIGVSTALEMILTGKQLRAKQALKLGLVDDVVPH--- 191

Query: 228 GIKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLTSYAMTIPFVRQQVYKTVE 287
                       L E AV  AK    ++  + +   + E++    +  P  R  ++K V 
Sbjct: 192 ----------SILLEAAVELAK----KERPSSRPLPVRERI----LAGPLGRALLFKMVG 233

Query: 288 EKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGELALTKESKALMGLYNGQV 347
           +K + +T+G YPA  +I++ V+TGL QG  +GY AE+  FGELA+T +S+AL  ++    
Sbjct: 234 KKTEHKTQGNYPATERILEVVETGLAQGTSSGYDAEARAFGELAMTPQSQALRSIFFAST 293

Query: 348 LCKKNKFG-APQKTVQQLAILGAGLMGAGIAQVSVDK-GLKTLLKDTTVTGLGRGQQQVF 405
             KK+    AP   +  + ILG GLMG GIA V+  K G+   +KD    G+    +  +
Sbjct: 294 DVKKDPGSDAPPAPLNSVGILGGGLMGGGIAYVTACKAGIPVRIKDINPQGINHALKYSW 353

Query: 406 KGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLAVKHKVLKEVESV 465
             L  KV+++ L + ERD   + + G  DY+GF   D++IEAVFE+L +K +++ EVE  
Sbjct: 354 DQLEGKVRRRHLKASERDKQLALISGTTDYRGFAHRDLIIEAVFENLELKQQMVAEVEQN 413

Query: 466 TPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQLLEIITTDKTSKDTTASA 525
              H IFASNTS+LPI  IAA + RPE+VIG+H+FSPV+KM L+EII    TS  T A+ 
Sbjct: 414 CAAHTIFASNTSSLPIGDIAAHATRPEQVIGLHFFSPVEKMPLVEIIPHAGTSAQTIATT 473

Query: 526 VAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLDALTTGFGFPVGAA 585
           V +  KQGK  IVV+D  GFY  R LAP ++E IR+L +G   + +DA    FGFPVG  
Sbjct: 474 VKLAKKQGKTPIVVRDKAGFYVNRILAPYINEAIRMLTQGERVEHIDAALVKFGFPVGPI 533

Query: 586 TLADEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMVSKGFLGRKSGKGFYIYQSGSKN 645
            L DEVGID    +   L  A+GERF      ++  +++    GRK+G+GFY+Y  G K 
Sbjct: 534 QLLDEVGIDTGTKIIPVLEAAYGERF-SAPANVVSSILNDDRKGRKNGRGFYLY--GQKG 590

Query: 646 KNLNSEIDNILVNLRLPAKPEVSSDEDIQYRVITRFVNEAVLCLQEGILATPEEGDIGAV 705
           +    ++D  +  L         S   +  R +   +NEAV C+ E ++ +  +GDIGAV
Sbjct: 591 RKSKKQVDPAIYPLIGTQGQGRISAPQVAERCVMLMLNEAVRCVDEQVIRSVRDGDIGAV 650

Query: 706 FGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQFTPCQLLRDL 753
           FG+GFPP LGGPFR++D  GA +VV  +++  + YG++FTPC+ L ++
Sbjct: 651 FGIGFPPFLGGPFRYIDSLGAGEVVAIMQRLATQYGSRFTPCERLVEM 698


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: 1095
Number of extensions: 43
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: 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 (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 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