GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadB in Acidovorax sp. GW101-3H11

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Ac3H11_1914 Enoyl-CoA hydratase (EC 4.2.1.17) / 3,2-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35)

Query= BRENDA::Q0KEG0
         (807 letters)



>lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1914 Enoyl-CoA hydratase
           (EC 4.2.1.17) / 3,2-trans-enoyl-CoA isomerase (EC
           5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35)
          Length = 800

 Score =  974 bits (2519), Expect = 0.0
 Identities = 500/810 (61%), Positives = 611/810 (75%), Gaps = 13/810 (1%)

Query: 1   MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKEGPKNGIALRAIENLKKLSP 60
           MS F VKKVAVLGAGVMGAQIAAHL+N +VPVVLFDLPAKEGPKNGI  +A+E LKKL P
Sbjct: 1   MSRFQVKKVAVLGAGVMGAQIAAHLVNVKVPVVLFDLPAKEGPKNGIVTKAVEGLKKLKP 60

Query: 61  APLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFAT 120
           +PLG+ ++A LIQ ANYE+ + LLKECDLVIEAIAERMDWK DLY K+APH+A HAI A+
Sbjct: 61  SPLGLADDAALIQQANYEEHMHLLKECDLVIEAIAERMDWKLDLYTKIAPHVAKHAILAS 120

Query: 121 NTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTT 180
           NTSGLSIT LS+     +K RFCG+HFFNPPRYM LVELI T TTQP++LDQLEAF+T+ 
Sbjct: 121 NTSGLSITKLSEVLPESIKPRFCGIHFFNPPRYMTLVELINTPTTQPEVLDQLEAFVTSG 180

Query: 181 LGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTA 240
           LGKGVVRA DTPNF+ANRVGI  +LA   E E FG+ +DVVDDLTG KLGRA S TFRTA
Sbjct: 181 LGKGVVRAHDTPNFVANRVGIAGMLATMKEVENFGLTYDVVDDLTGKKLGRASSGTFRTA 240

Query: 241 DVVGLDTMAHVIKTMQDTL--HDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKEGKA 298
           DVVGLDTMAHVIKT+QD L    DPF   + TPAVLK L++ G LGQK  AGF+KK G+ 
Sbjct: 241 DVVGLDTMAHVIKTLQDNLSIETDPFYESFGTPAVLKKLLELGNLGQKAKAGFFKKVGRD 300

Query: 299 IKVLDAKTGQYVDAGKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIA 358
           +   +  + +YV AG+KADE+  RMLKK AAER++LLR +     QFLWA+ R+ FHY A
Sbjct: 301 VMRFELDSEEYVPAGQKADEVYSRMLKKPAAERLRLLRNAEGAPGQFLWAILRNSFHYAA 360

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

Query: 419 WVFEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKG-TAAADPRKAGRT 477
           WVF+GPVAE  GVH A GSWS +   FV R +LPVY+RQ F  A+ G T+  D R AG T
Sbjct: 421 WVFKGPVAEAAGVHTAQGSWSASQNKFVPRRQLPVYERQIFPEALLGETSLPDWRTAGTT 480

Query: 478 VEENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSL 537
           + E+ A+R W  +GQ  VL+ S K+KM+ I P+V++ L  A++LAE+ Y+G+V+W     
Sbjct: 481 IAESKALRTWTLDGQ--VLIASIKNKMHAISPEVMEALMEALELAESEYQGMVIW----- 533

Query: 538 QLGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIAL 597
              +   PFS GA+LEA MPAFM+GGA  +E   +  Q+ MMR++YA VPVV+A  G+AL
Sbjct: 534 ---SGDAPFSVGADLEATMPAFMVGGADAVESIEQELQNLMMRIRYAQVPVVAAIHGMAL 590

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

Query: 658 TSRFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPT 717
           T  F +AAMAKV  SALE+R++G+L   D IV +  ELL+VA NE +++A++G+ AP   
Sbjct: 651 TEGFTAAAMAKVGTSALESRKLGFLLDGDVIVPHKDELLFVAINEAKSMAASGWCAPHKR 710

Query: 718 LVPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLAL 777
           L PVAGRSG+ATIKA LVNMRDGGFIS +DF I + IAE VCGGDV+AGS+VSE++LL L
Sbjct: 711 LFPVAGRSGLATIKAQLVNMRDGGFISAYDFKIGAMIAEVVCGGDVDAGSMVSEEYLLTL 770

Query: 778 ERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           ERK F  L+   KT ERI+GML TGKPVRN
Sbjct: 771 ERKVFCHLIAQPKTHERILGMLSTGKPVRN 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: 1599
Number of extensions: 62
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 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