GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Desulfoscipio geothermicus DSM 3669

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_092482981.1 BM299_RS08140 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_900115975.1:WP_092482981.1
          Length = 807

 Score =  488 bits (1255), Expect = e-142
 Identities = 313/828 (37%), Positives = 443/828 (53%), Gaps = 51/828 (6%)

Query: 6   VKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAK-------------EGP--KNGIALR 50
           + K AVLGAGVMGA IAAHL N  +P  L D+                E P  +N +A  
Sbjct: 5   INKAAVLGAGVMGATIAAHLANVGIPTYLLDIVPNQLTPEEEKKGLTLESPQVRNRLATG 64

Query: 51  AIENLKKLSPAPLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAP 110
           AI  + K  PAP  + E A L+   N+ED++ +L ECD +IE + ER+D K  L+KKV  
Sbjct: 65  AIGAMLKAKPAPFYVPENAALLTPGNFEDNMDVLAECDWIIEVVVERLDIKQSLFKKVEA 124

Query: 111 HLASHAIFATNTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQIL 170
                +I A+NTSG+SI  + +G   + K  F G HFFNPPRYM L+ELIP + T P++L
Sbjct: 125 VRRPGSIVASNTSGISINKMCEGLSQEFKQHFLGAHFFNPPRYMKLLELIPCSETLPEVL 184

Query: 171 DQLEAFLTTTLGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLG 230
           + +  F    LGKGVV  KDTPNFIANR+G++ + A       FG+  + VD LTG  L 
Sbjct: 185 EFMRDFGERILGKGVVICKDTPNFIANRIGVYGMCATIKAMLDFGLTVEEVDALTGRALC 244

Query: 231 RAKSATFRTADVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAG 290
           R KSA+FRT D+VGLD M HV K + D   +     V++TP  L+ +++   LG KT  G
Sbjct: 245 RPKSASFRTLDMVGLDVMVHVAKNVYDVATEPAEKAVFETPEFLQKMLENKWLGDKTKQG 304

Query: 291 FYKK----EGKAIKVLDAKTGQYVDAGK-KADEIVVRMLKKDAAERIKLLRESTNPQAQF 345
           FYKK    +G+ I VLD    +Y    K K   +         A+++K L    +  A+F
Sbjct: 305 FYKKVKTDKGREILVLDYNAMEYRPKEKPKFASLEAAKQAGKPAKQMKTLVFGKDKGAEF 364

Query: 346 LWAVFRDVFHYIAVYLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAEWVKEDV 405
            W V ++   Y A  L +IA     ID A++WGF W+ GPFE W   G ++VA+ +K + 
Sbjct: 365 AWRVQKETIVYAANLLGEIADDIQSIDDAMKWGFNWDFGPFEVWDILGVQEVADRIKAE- 423

Query: 406 EAGKALSAAPLPAWVFEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKG 465
                     +P  V E   A   G +     +      F   SK  V +R       +G
Sbjct: 424 -------GGTVPKVVEELLAAGRTGFYEKKDGY---RYYFEQNSKESVRER-----IPEG 468

Query: 466 TAAADPRKAGRTVEENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAG 525
                P K    V ++++    +  G D V  + F SK N IG D+++ +  ++   E  
Sbjct: 469 IIFLAPLKEQNKVIKSNSGASLIDIG-DGVACLEFHSKANAIGDDIVNMINYSVKEVEQN 527

Query: 526 YKGLVVWQPTSLQLGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYAS 585
           Y+GLV+        G  G  FS GANL   +          ++  V  FQ   MR+KY  
Sbjct: 528 YEGLVI--------GNFGQHFSVGANLFLILMEAEDDEFDELDIMVDEFQKANMRLKYCK 579

Query: 586 VPVVSAASGIALGGGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAA--- 642
            PVV+A  G+ +GGGCE+ LH+    AA ETY+GLVEVGVGLVP GGG KE A  AA   
Sbjct: 580 KPVVAAPHGMTVGGGCEVCLHAHRVNAAGETYMGLVEVGVGLVPGGGGCKELAFRAAELM 639

Query: 643 --RAAQAAGSTNILQFLTSR-FQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVA 699
             ++    G TN +Q + +R F++ AMAKV+ S  EA + GY++P+D++  N   ++  A
Sbjct: 640 PPKSQVTTGGTNTVQPMINRAFENIAMAKVATSGYEAIKFGYMRPTDRVSPNRDRIIGDA 699

Query: 700 QNEVRALASAGYRAPLPTLVPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVC 759
           +  V  +A+ G++   P  +   G +G A I+  +  +  G  IS HD  IA ++A  + 
Sbjct: 700 KRMVLQMAANGFKPLQPKKMQAVGNAGYAAIELGIQTLLWGKQISEHDAKIAKKVAYILT 759

Query: 760 GGDVEAGSLVSEDWLLALERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           GG V  G+ V+E  LL LER+AF+ LLG  KT +R+  ML+  KP+RN
Sbjct: 760 GGGVTPGTEVTEQDLLDLEREAFLSLLGEPKTLDRMRYMLKYNKPLRN 807


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: 1332
Number of extensions: 55
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: 807
Length of database: 807
Length adjustment: 41
Effective length of query: 766
Effective length of database: 766
Effective search space:   586756
Effective search space used:   586756
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: 56 (26.2 bits)

This GapMind analysis is from Apr 09 2024. 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