Alignments for a candidate for ech in Leeuwenhoekiella blandensis MED217

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Leeuwenhoekiella blandensis MED217

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_009779948.1 MED217_RS07760 3-hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase family protein

Query= BRENDA::Q0KEG0
         (807 letters)



>NCBI__GCF_000152985.1:WP_009779948.1
          Length = 802

 Score =  466 bits (1198), Expect = e-135
 Identities = 304/843 (36%), Positives = 436/843 (51%), Gaps = 77/843 (9%)

Query: 1   MSNFIVKKVAVLGAGVMGAQIAAHLINARVPVVLFDLPAKE---------------GPKN 45
           MS   + KVAV+G+G+MG+ IA H  N  V V+L D+  +E                 +N
Sbjct: 1   MSKRRINKVAVIGSGIMGSGIACHFANIGVEVLLLDIVPRELNDKEKAKGLTLDDKTVRN 60

Query: 46  GIALRAIENLKKLSPAPLGIKEEAGLIQAANYEDDIALLKECDLVIEAIAERMDWKHDLY 105
            +    ++N  K  P+P+  K+ A  I   N EDDIA +K+ D +IE + ER+D K  ++
Sbjct: 61  RLVNDHLQNALKSKPSPIYHKDFAKRITTGNMEDDIAKVKDYDWIIEVVIERLDIKKQVF 120

Query: 106 KKVAPHLASHAIFATNTSGLSITALSDGFDADLKSRFCGVHFFNPPRYMHLVELIPTATT 165
           +K+  H     +  +NTSG+ I  +S+G   D +  FCG HFFNP RY+ L E+IP   T
Sbjct: 121 EKLDKHRTPGTLITSNTSGIPIKFMSEGRSDDFQKHFCGTHFFNPARYLDLFEIIPGPNT 180

Query: 166 QPQILDQLEAFLTTTLGKGVVRAKDTPNFIANRVGIFSILAVFAEAEKFGIPFDVVDDLT 225
             ++L  L A+    LGK  V AKDTP FI NRVG +SI+++F   E+ G+  + VD LT
Sbjct: 181 DKEVLAFLNAYGEKFLGKTSVVAKDTPAFIGNRVGTYSIMSLFHTVEELGMTVEEVDKLT 240

Query: 226 GSKLGRAKSATFRTADVVGLDTMAHVIKTMQDTLHDDPFAPVYKTPAVLKGLVDAGALGQ 285
           G  +GR KSATFRT DVVGLDT+ HV   +++ + +D  A ++  P  +  + +   LG 
Sbjct: 241 GPVIGRPKSATFRTVDVVGLDTLVHVANGIRENVENDERAELFSLPNYINTMHENKWLGS 300

Query: 286 KTGAGFYKKEGK-----AIKVLDAKTGQYVDAGKKADEIVVRMLKK--DAAERIKLLRES 338
           KTG GFYKK  K      I  LD  + +Y  A K+A    + M K   + A+R  +L + 
Sbjct: 301 KTGQGFYKKIKKEDGSSEILTLDLNSMEY-RANKRASFSTLEMTKSIDNVADRFPVLVKG 359

Query: 339 TNPQAQFLWAVFRDVFHYIAVYLEQIAGSAADIDLAIRWGFGWNSGPFEDWQSAGWK--- 395
            +   +F    F  +F Y+   + +I      ID A+R G+GW  GPF+ W + G +   
Sbjct: 360 KDKAGEFFRKNFAGLFAYVQNRIPEITDELYKIDDAMRAGYGWEHGPFQIWDAVGVEKGI 419

Query: 396 --------QVAEWVKEDVEAGKALSAAPLPAWVFEGPVAENQGVHAAAGSWSPATQSFVA 447
                   +VA+WV   + +GK           F   + + + V        P    F+ 
Sbjct: 420 ELMKAEGYEVADWVAAMLSSGKDSFYTVKEGNTFYYDIPKKEYVK------KPGQDGFI- 472

Query: 448 RSKLPVYQRQAFRAAIKGTAAADPRKAGRTVEENDAVRIWVSEGQDDVLVVSFKSKMNTI 507
                                 D  +  + V +N  V   V +  D +L V F+SKMN+I
Sbjct: 473 --------------------ILDNIRESKEVFKNSGV--VVEDLGDGILNVEFRSKMNSI 510

Query: 508 GPDVIDGLTRAIDLAEAGYKGLVVWQPTSLQLGAPGGPFSAGANLEAAMPAFMMGGAKGI 567
           G DV+ GL RAIDLAE  + GLVV           G  FS GAN+       +      +
Sbjct: 511 GGDVLSGLNRAIDLAEKDFAGLVV--------ANQGKNFSVGANIGMIFMMAVEQEYDEL 562

Query: 568 EPFVKRFQDGMMRVKYASVPVVSAASGIALGGGCELMLHSASRVAALETYIGLVEVGVGL 627
              VK FQD  MR++Y+S+P V A   + LGGGCE+ LH+   VAA E+YIGLVE GVG+
Sbjct: 563 NAAVKYFQDTCMRLRYSSIPTVVAPQAMTLGGGCEMTLHADRVVAAAESYIGLVEFGVGV 622

Query: 628 VPAGGGLKEAALAAARAAQAAGSTNI-LQFLTSRFQSAAMAKVSASALEARQMGYLQP-S 685
           +P GGG KE  L   RA++     ++ L  L   F +  MAKVS SA EA  +G L+P  
Sbjct: 623 IPGGGGSKEMTL---RASETYHKDDVELNRLREYFLTIGMAKVSTSAYEAYDLGILKPGK 679

Query: 686 DKIVFNVHELLYVAQNEVRALASAGYRAPLP-TLVPVAGRSGIATIKASLVNMRDGGFIS 744
           D +V N    +  A+   + +A  GY  P+  T + V G+  +         M  G +IS
Sbjct: 680 DIVVVNKDRQIAAAKEVAKFMADQGYTKPIERTDIKVLGKQALGAFLVGTDQMNAGKYIS 739

Query: 745 THDFLIASRIAEAVCGGDVEAGSLVSEDWLLALERKAFVDLLGTGKTQERIMGMLQTGKP 804
            HD  IA+++A  + GGD+   S VSE +LL LER+AF+ L G  KT ER+  M++ GKP
Sbjct: 740 DHDQKIANKLAYVMAGGDLSEASYVSERYLLDLEREAFLSLCGERKTLERLEHMIKKGKP 799

Query: 805 VRN 807
           +RN
Sbjct: 800 LRN 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: 1286
Number of extensions: 65
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
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 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 2024 update 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