GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1914
          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:

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