GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Halioglobus japonicus S1-36

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_084198499.1 C0029_RS14200 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::A4YDS4
         (651 letters)



>NCBI__GCF_002869505.1:WP_084198499.1
          Length = 718

 Score =  171 bits (433), Expect = 1e-46
 Identities = 124/400 (31%), Positives = 190/400 (47%), Gaps = 30/400 (7%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVE 61
           K+ ++G+GVMG GIA  AA  G  V + D++ E   +       +  K R     ++  E
Sbjct: 322 KLGILGAGVMGAGIAFNAAKVGMNVVLKDLTQENADKGKAYAASACEKSRRID--EQQAE 379

Query: 62  QVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPIS 121
           ++L RI P  D A  L   D VIEAV E+ ++K  + R  EA     AV A+NTS+LPI+
Sbjct: 380 EILGRIQPTADVAD-LADCDLVIEAVFENRDVKAAVTRETEAVLGEQAVFASNTSALPIT 438

Query: 122 EIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDV 181
           E+A     PQ  +GMHFF+P   MPLVEI+ G+ TSDE +    ++A+ M K+ IVVKD 
Sbjct: 439 ELAQASVRPQNFIGMHFFSPAERMPLVEIITGEQTSDECLAWAFDLAQKMGKKPIVVKDA 498

Query: 182 PGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVW 241
           PGFF  RV+ + +  G  ++ +G+      + +A    G PMG     D   L+  Y   
Sbjct: 499 PGFFTTRVIGQTITQGQRMLAEGVNPALIENGAAFN--GSPMGPLETLDTISLETAYHAA 556

Query: 242 KA----VTARGFKAFPCSSTE----KLVSQGKLGVKSGSGYYQYPSPGKFVR--PTLPST 291
                   ARG +  P + +E     +    ++G   G+G+Y Y   GK V     L + 
Sbjct: 557 NQQRVDAEARGEQVEPSAESEVIRIMVEEAERVGQAKGAGFYDYDDNGKKVATWAGLKAL 616

Query: 292 SKKLG-----------RYLISPAVNEVSYLLREGIVGKDDAEKGCVLGLGLPK---GILS 337
             K G           R L S  +  +  +    +    D   G ++G+G P    G+  
Sbjct: 617 FAKDGYKDVPYQDVKDRLLFSQVLEAIRIMEEGVLTSVGDGNIGSIMGIGFPPHTGGVYQ 676

Query: 338 YADEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377
             +  G+    +  +E+    G + + P  LLL M  +G+
Sbjct: 677 CVNAYGVQAFADRAKELAAAYG-EAFEPPQLLLDMAADGR 715



 Score = 77.8 bits (190), Expect = 2e-18
 Identities = 57/172 (33%), Positives = 91/172 (52%), Gaps = 12/172 (6%)

Query: 419 NAINGDMIREINQALDSLEERED-VRVIAI-TGQGRVFSAGADVTEFGSLTPVKAMIASR 476
           N +  +    + +ALD LE   D ++ + I +G+   F AG D+T    +    +     
Sbjct: 26  NVMGEEYAEAMPKALDELEAMGDELKGLYIRSGKPGQFFAGGDITMMLEMDLNPSQEERE 85

Query: 477 KFH-------EVFMKIQFLTKPVIAVINGLALGGGMELALSADFRVA--SKTAEMGQPEI 527
           + H       E   +I+ L  PV   ING ALGGG E+AL+  +R+A  S   ++G PE 
Sbjct: 86  EMHRGLLDAKEPLARIERLGVPVAVGINGPALGGGYEIALACHYRIAMDSPKVKVGLPEA 145

Query: 528 NLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFLAEPEE 578
            LGL+PG GG  R++R+ G ++ L L+  G+++ A +A   G++  LA  EE
Sbjct: 146 MLGLLPGAGGIVRMTRMLGMQEALGLISQGKQLVAAKALEKGLIHELAADEE 197


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: 1040
Number of extensions: 54
Number of successful extensions: 5
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: 651
Length of database: 718
Length adjustment: 39
Effective length of query: 612
Effective length of database: 679
Effective search space:   415548
Effective search space used:   415548
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:

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