Alignments for a candidate for ech in Nocardioides daejeonensis MJ31

GapMind for catabolism of small carbon sources

Alignments for a candidate for ech in Nocardioides daejeonensis MJ31

Align 3-hydroxybutyryl-CoA dehydrogenase (EC 1.1.1.157); 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35); short-chain-enoyl-CoA hydratase (EC 4.2.1.150) (characterized)
to candidate WP_110207906.1 DNK54_RS14955 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::A4YDS4
         (651 letters)



>NCBI__GCF_003194585.1:WP_110207906.1
          Length = 737

 Score =  158 bits (399), Expect = 9e-43
 Identities = 127/401 (31%), Positives = 193/401 (48%), Gaps = 34/401 (8%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAME-RIKWSLSKLRESGSLKEGV 60
           KV V+G+G+MG GIA  AA AG +V + D +    ++      K     +      +E  
Sbjct: 337 KVGVVGAGMMGAGIAYAAARAGIDVVLMDTTLAGAEKGRAYSAKVEGRAVARGQRTQEAA 396

Query: 61  EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120
           +QV+ARI   TD  Q L G DFVIEAV E+  LK  +F + E      AVL +NTS+LPI
Sbjct: 397 DQVVARI-TATDDVQDLAGVDFVIEAVFENAALKAEVFASVEQVVGAEAVLGSNTSTLPI 455

Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180
           S +A+ +  PQ  VG+HFF+P   MPLVEI+RG+ TSD  +    ++   + K  IVV D
Sbjct: 456 SSLAAGVARPQDFVGVHFFSPVDRMPLVEIIRGEATSDATLAKAFDLVLQLGKTPIVVND 515

Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGI--ASIQEVDSSAIEELGFPMGVFLLADYTGLDIGY 238
             GFF +RV++  +     +V +G+   SI++    A    G+P G   L D   L +  
Sbjct: 516 SRGFFTSRVIIARLNEAVAMVGEGVPCPSIEQASLQA----GYPAGALQLLDELTLTLPR 571

Query: 239 SVWKAVTARG------FKAFPCSST-EKLVSQ-GKLGVKSGSGYYQYPSPGKF------- 283
           +V +   A        + A P  +  ++L+ + G++G   G G+Y Y   GK        
Sbjct: 572 AVREEAKAAAEAAGLDWLAHPSHAIFDRLIDEFGRVGRAGGGGFYDYDDQGKRTGFWPGL 631

Query: 284 -----VRPTLPSTSKKLGRYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPK---GI 335
                   T+P     + R L +  +   +  +   I    DA  G +LG+G P    G+
Sbjct: 632 ASSFPTLDTMPPLPDLVDRLLFAEVLEAWAAHVAGVIEAPSDANVGSLLGIGFPAWTGGV 691

Query: 336 LSYADEI--GIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVK 374
           L + D+   G    V   E++    G D + P   LL  ++
Sbjct: 692 LRFLDQYDGGRAGFVARAEQLAARYG-DRFLPPATLLETLE 731



 Score = 93.2 bits (230), Expect = 4e-23
 Identities = 62/183 (33%), Positives = 100/183 (54%), Gaps = 9/183 (4%)

Query: 402 RVEPPLAWIVLNRPTR-YNAINGDMIREINQALDSLE-EREDVRVIAITGQGRVFSAGAD 459
           R E  +  + L+ PT+  N ++   + E+   ++ L+ ERE +  + IT     F AG D
Sbjct: 26  RDEDGVVVVTLDDPTQEVNTVHTGFVHELGALVEHLQAEREGLAGVVITSAKSTFVAGGD 85

Query: 460 VTEFGSLTPVKAMIASRKFHEV---FMKIQFLTKPVIAVINGLALGGGMELALSADFRVA 516
           + E  +L    A   +R  + +      ++ L  PV+A ING ALGGG+ELAL+A  R+ 
Sbjct: 86  LNEIVTLGLADAARFTRHLNNLKATLRTLETLGVPVVAAINGSALGGGLELALAAHHRIV 145

Query: 517 --SKTAEMGQPEINLGLIPGGGGTQRLSRLSGRKGL--ELVLTGRRVKAEEAYRLGIVEF 572
             S   ++G PE+ LGL+P  GG  R  R+ G +    E++L+GRR +  +A  LG+V+ 
Sbjct: 146 VDSPRVQLGLPEVGLGLLPASGGIVRTVRMLGAQRALDEVLLSGRRFRPTQARDLGLVDE 205

Query: 573 LAE 575
           L +
Sbjct: 206 LVD 208



 Score = 27.7 bits (60), Expect = 0.002
 Identities = 24/97 (24%), Positives = 44/97 (45%), Gaps = 8/97 (8%)

Query: 299 LISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMR--- 355
           +I   +NE   ++ EG+      +    L  G P G L   DE+ + +     EE +   
Sbjct: 524 VIIARLNEAVAMVGEGVPCPSIEQAS--LQAGYPAGALQLLDELTLTLPRAVREEAKAAA 581

Query: 356 QTSGMDHYS-PDPLLLSMVKE--GKLGRKSGQGFHTY 389
           + +G+D  + P   +   + +  G++GR  G GF+ Y
Sbjct: 582 EAAGLDWLAHPSHAIFDRLIDEFGRVGRAGGGGFYDY 618


Lambda     K      H
   0.316    0.134    0.377 

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: 1006
Number of extensions: 58
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 651
Length of database: 737
Length adjustment: 39
Effective length of query: 612
Effective length of database: 698
Effective search space:   427176
Effective search space used:   427176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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:

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