GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Dyella japonica UNC79MFTsu3.2

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 N515DRAFT_0416 N515DRAFT_0416 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxybutyryl-CoA epimerase

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0416
          Length = 686

 Score =  175 bits (444), Expect = 5e-48
 Identities = 121/370 (32%), Positives = 184/370 (49%), Gaps = 16/370 (4%)

Query: 3   VTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVEQ 62
           V V+G+GVMG  IA  AA  G +V + D   + +Q A++R +    K  ++    E VE+
Sbjct: 311 VHVVGAGVMGGDIAAWAAFKGFQVTLQDREMKFIQPALDRARALYEKKLKT---PEKVEE 367

Query: 63  VLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPISE 122
              R+  + +  + +  +D  IEA+ E+ E K+ ++ + E       +LATNTSS+P+ E
Sbjct: 368 TARRLRADVE-GKGVAAADLAIEAIFENAEAKQALYASIEPQFQADEILATNTSSIPLDE 426

Query: 123 IASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDVP 182
           +   LK+PQR +G+HFFNP   MPLVE+VR      EV K      K++ K  + VK  P
Sbjct: 427 LRRGLKAPQRFLGLHFFNPVAQMPLVEVVRHDGLDPEVEKRALAFCKAIGKLPVAVKGTP 486

Query: 183 GFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVWK 242
           GF VNR+L+  +     L  +G+     V     ++ G PMG   LAD  GLD+  SV K
Sbjct: 487 GFLVNRILMPYLLEAIRLYNEGVPG--PVLDKEAKKFGMPMGPIELADTVGLDVCASVGK 544

Query: 243 AVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQYPSPGKFVRPTLP---STSKKLGRYL 299
            +        P    +KL + GK G K G G+Y +   GK  +P +    +    L   +
Sbjct: 545 ELAPFLGLELPPGIEDKLAA-GKRGKKDGQGFYVW-QEGKPQKPEVDPDYAVPADLQERM 602

Query: 300 ISPAVNEVSYLLREGIVGKDD-AEKGCVLGLGLPK---GILSYADEIGIDVVVNTLEEMR 355
           + P VNE    L +G+V   D  + G + G G      G + Y    G  V+   LE + 
Sbjct: 603 LLPMVNEAVACLADGVVDDADLLDAGVIFGTGFAPFRGGPIQYVRSEGAAVIKGKLERLA 662

Query: 356 QTSGMDHYSP 365
           Q  G + ++P
Sbjct: 663 QRHG-ERFTP 671



 Score = 94.0 bits (232), Expect = 2e-23
 Identities = 59/172 (34%), Positives = 94/172 (54%), Gaps = 4/172 (2%)

Query: 419 NAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSLTPVKAMIAS-RK 477
           NA++ +++ E+ Q ++ L   +   V+  + +   F+ GAD+ EF        ++ +   
Sbjct: 32  NALSREVLDELGQIVERLSIEKPAGVLIHSAKPGGFAVGADIKEFVEYARDGTVLQNIEN 91

Query: 478 FHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVAS--KTAEMGQPEINLGLIPGG 535
              VF  +  L  P +A I+G  +GGG EL L+   R+A+  +   +G PE+ LG+ PG 
Sbjct: 92  GQRVFESLARLPCPTVAAIHGACMGGGTELVLACRQRIAADDEKTRIGLPEVMLGIHPGW 151

Query: 536 GGTQRLSRLSGR-KGLELVLTGRRVKAEEAYRLGIVEFLAEPEELESEVRKL 586
           GGT RL RL G    L ++LTG+ + A  A  LG+V+ LA P EL +E R L
Sbjct: 152 GGTARLPRLIGALDALPVMLTGKALSARRAAALGVVDRLAPPNELLAEARAL 203



 Score = 41.2 bits (95), Expect = 2e-07
 Identities = 27/94 (28%), Positives = 47/94 (50%), Gaps = 11/94 (11%)

Query: 299 LISPAVNEVSYLLREGIVGK---DDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMR 355
           ++ P + E   L  EG+ G     +A+K      G+P G +  AD +G+DV  +  +E+ 
Sbjct: 493 ILMPYLLEAIRLYNEGVPGPVLDKEAKK-----FGMPMGPIELADTVGLDVCASVGKELA 547

Query: 356 QTSGMDHYSPDPLLLSMVKEGKLGRKSGQGFHTY 389
              G++     P +   +  GK G+K GQGF+ +
Sbjct: 548 PFLGLEL---PPGIEDKLAAGKRGKKDGQGFYVW 578


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: 962
Number of extensions: 57
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: 686
Length adjustment: 38
Effective length of query: 613
Effective length of database: 648
Effective search space:   397224
Effective search space used:   397224
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 17 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:

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