Alignments for a candidate for ech in Methylosarcina fibrata AML-C10

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Methylosarcina fibrata AML-C10

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_020565869.1 A3OW_RS0123285 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_000372865.1:WP_020565869.1
          Length = 772

 Score =  394 bits (1013), Expect = e-114
 Identities = 274/810 (33%), Positives = 408/810 (50%), Gaps = 48/810 (5%)

Query: 6   VKKVAVLGAGVMGAQIAAHLINARVPVVLFDL-PAKEGPKNGIALRAIENLKKLSPAPLG 64
           ++KVAV+GAGVMGA IAAH+ NA +PVVL D+ P     ++ IA  A+E L K  P PL 
Sbjct: 3   IEKVAVIGAGVMGASIAAHISNAGIPVVLLDIVPENASDRSIIAKTAVEKLLKADPPPLM 62

Query: 65  IKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAPHLASHAIFATNTSG 124
                 LI   N EDD  LL + D VIEA+ E+   K  LY+K+        + ++NTS 
Sbjct: 63  HPGNIRLITPGNIEDDPGLLADVDWVIEAVVEQPQVKQSLYRKLETVCTKDCLISSNTST 122

Query: 125 LSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQILDQLEAFLTTTLGKG 184
           L ++ L+       + RF   HFFNPPRYM L+EL+    T+P++   +  F    LGK 
Sbjct: 123 LPLSLLTQDMPDSFRQRFMITHFFNPPRYMRLLELVSGPETRPELTAAVTRFADVRLGKN 182

Query: 185 VVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLGRAKSATFRTADVVG 244
            +  KDTP FI NR+GI+ +L    EA +  +  +V D    +  G  K+  F   D+VG
Sbjct: 183 CIACKDTPGFIGNRIGIYWLLCGLHEAIELNVSVEVADAAISAPFGIPKTGIFGLLDLVG 242

Query: 245 LDTMAHVIKTMQDTL-HDDPFAPVYKTPAVLKGLVDAGALGQKTGAGFYKKE---GKAIK 300
           LD + H++K+M+  L   D F  V + P V++ ++++G  G+K   GFY+     GK +K
Sbjct: 243 LDLVPHILKSMEQALPKTDAFHQVGRLPEVVRNMIESGHTGRKGKGGFYRLNEAGGKRVK 302

Query: 301 -VLDAKTGQYVDAGKKADEIVVRMLKKDAAERIKLLRESTNPQAQFLWAVFRDVFHYIAV 359
             ++  TG Y    +K D  +++  +K  A+    L  S +P A +   V      Y A 
Sbjct: 303 EAVNLATGDY-RVSEKPDLSLLQEAQKKGAQS---LLSSPDPAALYARRVMAKTLAYAAG 358

Query: 360 YLEQIAGSAADIDLAIRWGFGWNSGPFE--DWQSAGWKQVAEWVKEDVEAGKALSAAPLP 417
            + +I+     ID A+R GF W  GPF+  D    GW   A  + ED      L   PL 
Sbjct: 359 LVPEISDDITAIDAAMRDGFNWKLGPFQLIDQIGVGW--FAGALHED-----HLPVPPL- 410

Query: 418 AWVFEGPVAENQGVHAAAGSWSPATQSFVARSKLPVYQRQAFRAAIKGTAAADPRKAGRT 477
                  +A  Q ++ A            A   +P  + +   A IK        + G +
Sbjct: 411 -------LAMKQPLYKAESGQLHYLDLTGAYRSVPSVEGRLLLADIK--------RQGPS 455

Query: 478 VEENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVIDGLTRAIDLAEAGYKGLVVWQPTSL 537
           + EN +  +W  +  D V  + F SK+NT+  + +  + +++D     YK LV+      
Sbjct: 456 LLENRSASLW--DIGDGVACLEFHSKLNTLDMESMKLIRQSVDKVSESYKALVIHNDAE- 512

Query: 538 QLGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVKRFQDGMMRVKYASVPVVSAASGIAL 597
                   FSAGANL   M A        +E  ++  Q     +KYAS PVV+A SG+AL
Sbjct: 513 -------HFSAGANLGLLMEAIHRSDWHAVEQLIQEGQQTYKALKYASFPVVAAPSGLAL 565

Query: 598 GGGCELMLHSASRVAALETYIGLVEVGVGLVPAGGGLKEAALAAARAAQAAGSTNILQFL 657
           GGGCE++LH  +  A  E Y GLVEVGVGL+P  GG KE         +  G    +  +
Sbjct: 566 GGGCEILLHCDAIQAHAELYTGLVEVGVGLIPGWGGCKEYLRRWLAFPKRPGGP--IPPV 623

Query: 658 TSRFQSAAMAKVSASALEARQMGYLQPSDKIVFNVHELLYVAQNEVRALASAGYRAPLPT 717
              FQ+ +MA VS SA +A+++ +L  +D I  N   LL+ A+    +LA   Y  P P 
Sbjct: 624 VKAFQTISMATVSKSAADAKELLFLSRNDGITMNKDRLLFDAKARAISLAE-NYTPPSPP 682

Query: 718 LVPVAGRSGIATIKASLVNMRDGGFISTHDFLIASRIAEAVCGGDVEAGSLVSEDWLLAL 777
           + P+ G++    +   +   R  G  + +D  I  ++A  + GG+ +  + +SED LLAL
Sbjct: 683 VFPLPGKTVKILLSMGVKAYRLLGKATEYDVEIGDKLATVLSGGNTDITTPLSEDDLLAL 742

Query: 778 ERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           E +AFV L+    T  R+  ML+TGKP+RN
Sbjct: 743 ECEAFVALVKQPGTLARLEHMLKTGKPLRN 772


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: 1290
Number of extensions: 68
Number of successful extensions: 9
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: 772
Length adjustment: 41
Effective length of query: 766
Effective length of database: 731
Effective search space:   559946
Effective search space used:   559946
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources