GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_0416 N515DRAFT_0416
           3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase /
           3-hydroxybutyryl-CoA epimerase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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