GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Marivita geojedonensis DPG-138

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_085640004.1 MGEO_RS15835 FAD-dependent oxidoreductase

Query= BRENDA::A4YDS4
         (651 letters)



>NCBI__GCF_002115805.1:WP_085640004.1
          Length = 695

 Score =  173 bits (438), Expect = 3e-47
 Identities = 132/399 (33%), Positives = 202/399 (50%), Gaps = 29/399 (7%)

Query: 3   VTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGV-E 61
           V VIG G MG GIA    +AG  V + ++S +    A  RI  +LS   + G + +   +
Sbjct: 291 VAVIGGGTMGAGIATSFLLAGFPVTLLEMSEDAAHAARGRITGNLSGALKRGKIDQKTYD 350

Query: 62  QVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPIS 121
           ++       T     L+ +D VIEAV ED+ +KR +F   +A   P AVLATNTS L I+
Sbjct: 351 RLTGPALALTTSYDDLREADLVIEAVFEDMNVKRDVFSRLDAICKPGAVLATNTSYLDIN 410

Query: 122 EIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDV 181
           +IA   + P+ V+G+HFF+P  +M L+E+V    T+ + V T   +AK + K  +     
Sbjct: 411 KIADATQRPEDVIGLHFFSPAHVMKLLEVVVADRTAPDTVATGFALAKRLKKTAVRAGVC 470

Query: 182 PGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVW 241
            GF  NR+L     A  ++V  G A+  ++D +AI E GF MG F ++D  GLDI ++  
Sbjct: 471 DGFIGNRILAAYRAAADHMVLDG-ATPYDID-AAIREFGFAMGPFQVSDLAGLDIAWAAR 528

Query: 242 K--AVTARGFKAFPCSSTEKLVSQGKLGVKSGSGYYQY----PSPGKFVRPTLPSTSKKL 295
           K  A T    +  P  + ++L   G  G K+G GYY Y    P P   V   + S  + L
Sbjct: 529 KRRAATRDPRERVPLVA-DRLCEAGLFGQKTGQGYYLYNETPPKPNPEVAGIIESARETL 587

Query: 296 G-------------RYLISPAVNEVSYLLREGIVGKD-DAEKGCVLGLGLPK---GILSY 338
           G             RYL +  VNE + ++ +GI  +  D +   ++G G P+   G L +
Sbjct: 588 GIKPRAFSRPEIQRRYLCA-MVNEAAKVVGDGIARRPLDVDVVLLMGYGFPRYRGGPLKW 646

Query: 339 ADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377
           AD  G+  +++ +    Q      +SP PLL  +V EG+
Sbjct: 647 ADMDGLPKILSDITAYAQDDRY-FWSPAPLLEQLVAEGR 684



 Score =  107 bits (267), Expect = 2e-27
 Identities = 62/190 (32%), Positives = 115/190 (60%), Gaps = 9/190 (4%)

Query: 407 LAWIVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSL 466
           +A I ++ P   NA+   + + + +A++  E  +  R   I G+GR F AGAD+ EFG  
Sbjct: 13  IAMIAIDNPP-VNALGQAVRQGLVEAVEKAEA-DGARAALIYGEGRSFPAGADIREFGK- 69

Query: 467 TPVKAMIASRKFHEVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVASKTAEMGQPE 526
            P++  +      +V  +++     V++ ++G ALGGG+E+AL++D+R+A+  A++G PE
Sbjct: 70  PPLEPWLP-----DVCNRLETSPVLVVSALHGTALGGGLEIALASDYRIATPAAKVGLPE 124

Query: 527 INLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFLAEPEELESEVRK 585
           + +G++PG GGTQRL RL G    ++++ +GR++ A EA+ LGI++ + +    +  +  
Sbjct: 125 VLIGVMPGAGGTQRLPRLVGVETSIDVITSGRQISAGEAFDLGIIDRVEDGAPRDIGLSY 184

Query: 586 LANAIAEKSP 595
               +AE +P
Sbjct: 185 TRALLAENAP 194



 Score = 25.8 bits (55), Expect = 0.007
 Identities = 17/61 (27%), Positives = 28/61 (45%), Gaps = 3/61 (4%)

Query: 330 GLPKGILSYADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKE-GKLGRKSGQGFHT 388
           G   G    +D  G+D+        R+ +  D     PL+   + E G  G+K+GQG++ 
Sbjct: 507 GFAMGPFQVSDLAGLDIA--WAARKRRAATRDPRERVPLVADRLCEAGLFGQKTGQGYYL 564

Query: 389 Y 389
           Y
Sbjct: 565 Y 565


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: 942
Number of extensions: 56
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
Length of query: 651
Length of database: 695
Length adjustment: 39
Effective length of query: 612
Effective length of database: 656
Effective search space:   401472
Effective search space used:   401472
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.

Links

Downloads

Related tools

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