Alignments for a candidate for ech in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Pedobacter sp. GW460-11-11-14-LB5

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate CA265_RS17590 CA265_RS17590 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::Q0KEG0
         (807 letters)



>FitnessBrowser__Pedo557:CA265_RS17590
          Length = 802

 Score =  483 bits (1242), Expect = e-140
 Identities = 311/838 (37%), Positives = 446/838 (53%), Gaps = 77/838 (9%)

Query: 6   VKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKE---------------GPKNGIALR 50
           + KVAVLG+G+MG++IA H  N  V V+L D+  KE                 KN I   
Sbjct: 6   INKVAVLGSGIMGSRIACHFANIGVEVLLLDIAPKELSPEEQAKGLTLDNPAVKNRIVNT 65

Query: 51  AIENLKKLSPAPLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLYKKVAP 110
           A++   K +P+P+  K+    I+  N+ DD++ +   D VIE + E +D K  ++++V  
Sbjct: 66  ALQTAVKTNPSPVYTKKALNKIKTGNFADDMSKIAGYDWVIEVVVENLDIKKKVFEQVEQ 125

Query: 111 HLASHAIFATNTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATTQPQIL 170
                 +  +NTSG+ I  +++G   D K+ FCG HFFNPPRY+ L+E+IPT  TQP+I+
Sbjct: 126 FRKPGTLITSNTSGIPIHLMAEGRSEDFKAHFCGTHFFNPPRYLKLLEIIPTPHTQPEIV 185

Query: 171 DQLEAFLTTTLGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLTGSKLG 230
           D L  +    LGK  V  KDTP FIANRVG++SI+A+    EK  +  + VD  TG  LG
Sbjct: 186 DFLMHYGDKFLGKTTVLCKDTPAFIANRVGVYSIMALLHLVEKLDLTVEEVDKFTGPALG 245

Query: 231 RAKSATFRTADVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQKTGAG 290
           R KSATFRT+DVVGLDTM  V K + D   DD    ++K PA ++ + +   LG KT  G
Sbjct: 246 RPKSATFRTSDVVGLDTMIKVAKGLYDNCPDDKAHDLFKLPAYVQKMEENKWLGDKTQQG 305

Query: 291 FYKK----EGKA-IKVLDAKTGQYVDAGKKADEIVVRMLK--KDAAERIKLLRESTNPQA 343
           FYKK    +GK  I  LD KT +Y    +K     + M K  ++  ER+K+  +  +   
Sbjct: 306 FYKKTKSADGKTEILALDLKTLEY-KPQQKVKSATLEMTKPIENLRERMKIFAKGKDKAG 364

Query: 344 QFLWAVFRDVFHYIAVYLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWKQVAE---- 399
           +        +F Y++  + +I+     ID A+R GFGW  GPFE W + G K+  E    
Sbjct: 365 ELFRHSSFGLFEYVSDRIPEISDELYRIDDAMRAGFGWELGPFELWDAVGVKEAIEGMEQ 424

Query: 400 -------WVKEDVEAGKALSAAPLPAWVFEGPVAENQGVHAAAGSWSPATQSFVARSKLP 452
                  WV E ++AG          +  E  V +   + + +    P T  F+    L 
Sbjct: 425 YGNKAAAWVHEMLDAGNT------SFYKVENGVKKYYDIPSKSYKALPGTDEFIILDNL- 477

Query: 453 VYQRQAFRAAIKGTAAADPRKAGRTVEENDAVRIWVSEGQDDVLVVSFKSKMNTIGPDVI 512
                               +  +T+ +N  V I +  G D +L V F +KMNTIG DVI
Sbjct: 478 --------------------RENKTLWKNSGVSI-IDLG-DGILNVEFHTKMNTIGGDVI 515

Query: 513 DGLTRAIDLAEAGYKGLVVWQPTSLQLGAPGGPFSAGANLEAAMPAFMMGGAKGIEPFVK 572
            G+ +AID+AE  Y+GLV+        G  G  FSAGAN+       +      +   ++
Sbjct: 516 SGINKAIDMAEKDYRGLVI--------GNDGANFSAGANVGMIFMMAVEQEWDELNMAIR 567

Query: 573 RFQDGMMRVKYASVPVVSAASGIALGGGCELMLHSASRVAALETYIGLVEVGVGLVPAGG 632
            FQ+  MR++Y+S+PVV A   + LGGGCE  LH+     + ETY+GLVE GVG++P GG
Sbjct: 568 MFQNTSMRIRYSSIPVVVAPHNLTLGGGCEFSLHADHVQLSAETYMGLVEFGVGVIPGGG 627

Query: 633 GLKEAALAAARAAQAAGSTNILQ-FLTSRFQSAAMAKVSASALEARQMGYLQPSD-KIVF 690
           G KE AL   RA+       I+Q  L  RF +  MAKVS S  EA ++GYLQ     I  
Sbjct: 628 GTKEFAL---RASDEYKDDQIVQNALKDRFLTIGMAKVSTSGYEAYELGYLQKDKFSISM 684

Query: 691 NVHELLYVAQNEVRALASAGYRAPLP-TLVPVAGRSGIATIKASLVNMRDGGFISTHDFL 749
           N + LL  A+ +   LA AGY  P+    + V G+ G+  + A   +M  G FIS HD  
Sbjct: 685 NRNRLLADAKAKAIELADAGYTKPVQRNDIKVLGKQGLGIVYAGANSMYAGHFISEHDKK 744

Query: 750 IASRIAEAVCGGDVEAGSLVSEDWLLALERKAFVDLLGTGKTQERIMGMLQTGKPVRN 807
           I+ ++   +CGGD+ A + V+E +LL LER+AF+ L G  K+ ERI  ++  GKP+RN
Sbjct: 745 ISEKLGYVMCGGDLSAPTEVTEQYLLDLEREAFLSLAGERKSLERIQSIITKGKPLRN 802


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: 1377
Number of extensions: 74
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: 802
Length adjustment: 41
Effective length of query: 766
Effective length of database: 761
Effective search space:   582926
Effective search space used:   582926
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 Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Rules (tab-delimited)
Protein sequences (fasta format)
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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