GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Pseudarthrobacter sulfonivorans Ar51

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_058929311.1 AU252_RS02130 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

Query= BRENDA::A4YDS4
         (651 letters)



>NCBI__GCF_001484605.1:WP_058929311.1
          Length = 738

 Score =  175 bits (443), Expect = 8e-48
 Identities = 120/358 (33%), Positives = 181/358 (50%), Gaps = 12/358 (3%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGN-EVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGV 60
           K+ V+G+G+M   +A L A      V M DI    + + +  +   + KL     + +  
Sbjct: 350 KIGVVGAGLMASQLALLFARQLKVPVVMTDIDQARVDKGVGYVHAEVDKLLGKKRISQDA 409

Query: 61  EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120
                 +   +   +A   +DFVIEAV E+L +K+ +F   EA  SP  +LATNTSSL +
Sbjct: 410 ANRTRALVTGSVSKEAFADADFVIEAVFEELNVKKQVFAEVEAIVSPDCILATNTSSLSV 469

Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180
           + +A  L  P+R+VG HFFNP  +MPL+EIVR   T D V+ T  E+AK + K  ++VKD
Sbjct: 470 TAMAQDLAHPERLVGFHFFNPVAVMPLLEIVRAPKTDDAVLATAFELAKGLKKTAVLVKD 529

Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240
            P F VNR+LLR+M       ++G  +  EV  +++  +G PM  F L    GL +   V
Sbjct: 530 APAFVVNRILLRLMGEVTAAFDEGTPA--EVADTSLRPMGLPMTPFTLGAMVGLPVAQHV 587

Query: 241 WKAVTARGFKAFPCSST-EKLVSQG--KLGVKSGSGYYQYPSPGKFVRP--TLPSTSKKL 295
            +++ A     F  S+  +KL+  G   L V +  G  + P     +    T PST   +
Sbjct: 588 QESLHAAFGDRFAVSTNLQKLIENGVKSLWVPAADGSQEIPESTLSLMSFGTSPSTGDNV 647

Query: 296 GRYLISPAVNEVSYLLREGIV-GKDDAEKGCVLGLGLPK---GILSYADEIGIDVVVN 349
            R +      E+  +L EG+V G +D +   +LG G P    GI  Y D +G    VN
Sbjct: 648 LRRVQDALAEEIGLMLDEGVVAGPEDIDLCMILGAGWPMFLGGITPYLDRVGASERVN 705



 Score = 76.6 bits (187), Expect = 4e-18
 Identities = 56/175 (32%), Positives = 89/175 (50%), Gaps = 12/175 (6%)

Query: 428 EINQALDSLEERE---DVRVIAITGQGRVFSAGADVTEFGSL-TPVKAMIASRKFHEVFM 483
           E+   L+ L+ER    ++  + +TG+     AGAD++   SL      +  ++  H+V+ 
Sbjct: 64  ELGTVLEGLKERAARGEIVGVGVTGKPYFLVAGADLSAVKSLDNRDHGLWMAQLGHDVYA 123

Query: 484 KIQFLTKPVIAVINGLALGGGMELALSADFRVASKTA-EMGQPEINLGLIPGGGGTQRLS 542
            +  L  P  A ING+ALGGG+E+ L + +R  S  A  +  PE  +GL+PG GG   L 
Sbjct: 124 TLANLGVPSFAFINGVALGGGLEITLQSTYRTVSTGAGALALPEAFIGLVPGWGGVYILP 183

Query: 543 RLSGRKGLELVL------TGRRVKAEEAYRLGIVEFLAEPEE-LESEVRKLANAI 590
           RL G +    V+        R +   +A++LGI + L EP + LE  +   A  I
Sbjct: 184 RLIGPENAVKVMIENPLSNNRTLNGPQAFQLGIADALFEPADFLEQSLAWAATVI 238


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: 946
Number of extensions: 47
Number of successful extensions: 3
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: 738
Length adjustment: 39
Effective length of query: 612
Effective length of database: 699
Effective search space:   427788
Effective search space used:   427788
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 Apr 09 2024. 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