GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Acidovorax caeni R-24608

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_054256649.1 BN2503_RS10700 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_001298675.1:WP_054256649.1
          Length = 800

 Score =  981 bits (2537), Expect = 0.0
 Identities = 506/810 (62%), Positives = 615/810 (75%), Gaps = 13/810 (1%)

Query: 1   MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60
           MS F VKKVAVLGAGVMGAQIAAHL+N +VPVVLFDLPAKEGPK+ IA RAI NLKKL P
Sbjct: 1   MSRFNVKKVAVLGAGVMGAQIAAHLVNVKVPVVLFDLPAKEGPKSSIAERAIANLKKLKP 60

Query: 61  APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120
           +P+G+ E+A LIQAANYE+ + LLKECDLVIEAIAERMDWK DLY K+AP +A HAI A+
Sbjct: 61  SPIGVAEDADLIQAANYEEHLKLLKECDLVIEAIAERMDWKLDLYTKIAPFVAKHAIVAS 120

Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180
           NTSGLSIT LS+     +K RFCG+HFFNPPRYM LVELIPT TT+P +LDQLEAF+T+ 
Sbjct: 121 NTSGLSITKLSEALPEAIKPRFCGIHFFNPPRYMPLVELIPTPTTEPVVLDQLEAFVTSG 180

Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240
           LGKGVVRAKDTPNFIANR+GI  +L+   E E FG+ +DVVDDLTG KLGRA S TFRTA
Sbjct: 181 LGKGVVRAKDTPNFIANRIGIAGMLSTMKEVENFGLTYDVVDDLTGKKLGRASSGTFRTA 240

Query: 241 DVVGLDTMAHVIKTMQD--TLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKA 298
           DVVGLDTMAHVIKT+QD  +L  DPF   + TPAVL+ L++ G LGQKT AGF+KK G+ 
Sbjct: 241 DVVGLDTMAHVIKTLQDNLSLESDPFYGSFGTPAVLQKLIELGNLGQKTKAGFFKKVGRD 300

Query: 299 IKVLDAKTGQYVDAGKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIA 358
           I   + ++  YV AG+KAD++  RMLK+ AAER++LLR +     QFLWA+ R+ FHY A
Sbjct: 301 ILRFELESESYVPAGQKADDVYARMLKRPAAERLQLLRNAEGAPGQFLWAILRNSFHYAA 360

Query: 359 VYLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDVEAGKALSAAPLPA 418
           ++LE IA SA D+D A+RWGFG   GPFE WQ AGW +VA  V+ED++AGKAL  APLP 
Sbjct: 361 LHLETIADSARDVDQAMRWGFGMKQGPFELWQEAGWLEVARMVQEDIDAGKALCKAPLPK 420

Query: 419 WVFEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAA-ADPRKAGRT 477
           WVFEGPVA+  GVH A GSWSPA   FV R  LPVY+RQ F   + G A+  D + AG T
Sbjct: 421 WVFEGPVAQAGGVHTAEGSWSPALGKFVPRRVLPVYERQLFPEKLLGEASLPDWQTAGTT 480

Query: 478 VEENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSL 537
           + E+ A+R W  +GQ  VL+ S K+KM+ I P+V++GL  A++LAEA Y+G+V+W     
Sbjct: 481 LFESKALRTWTLDGQ--VLIASIKNKMHAISPEVMEGLVEAVELAEAEYQGMVIW----- 533

Query: 538 QLGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIAL 597
              +   PFS GA+LEA MPAF++GGA  IE   +  Q+ MMR++YA VPVV+A  G+AL
Sbjct: 534 ---SGDAPFSVGADLEATMPAFVVGGADAIESVEQELQNLMMRIRYAQVPVVAAIHGMAL 590

Query: 598 GGGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFL 657
           GGGCEL ++SA RVA +E+YIGLVEVGVGLVP  GGL   A  AA     + S ++L FL
Sbjct: 591 GGGCELAVYSARRVAHMESYIGLVEVGVGLVPGAGGLTYIARRAAENMAKSTSRDLLPFL 650

Query: 658 TSRFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPT 717
           T  F +AAMAKV  SA+E+R++GYL  SD IV +  E+L+VA NE +A+A+ G+RAPL  
Sbjct: 651 TEGFTAAAMAKVGTSAIESRKLGYLLDSDLIVPHKDEVLFVAINEAKAMAAGGWRAPLKR 710

Query: 718 LVPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLAL 777
           L PVAGRSG+ATIKA LVNMRDGGFIS +DF IAS I + VCGGDV+AGSLVSE++LL L
Sbjct: 711 LFPVAGRSGLATIKAQLVNMRDGGFISAYDFKIASMIGDVVCGGDVDAGSLVSEEYLLTL 770

Query: 778 ERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           ERK F  L+   KT ERI+GML TGKPVRN
Sbjct: 771 ERKVFCHLIAQPKTHERILGMLNTGKPVRN 800


Lambda     K      H
   0.319    0.134    0.391 

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: 1642
Number of extensions: 70
Number of successful extensions: 5
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: 807
Length of database: 800
Length adjustment: 41
Effective length of query: 766
Effective length of database: 759
Effective search space:   581394
Effective search space used:   581394
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 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