GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_1850 Enoyl-CoA hydratase [isoleucine degradation] (EC 4.2.1.17) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1850
          Length = 715

 Score =  194 bits (492), Expect = 2e-53
 Identities = 130/398 (32%), Positives = 206/398 (51%), Gaps = 26/398 (6%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEG-V 60
           K+ +IG+G+MG+GIA ++A  G EV + D+S E  ++    ++  LSK    G L E   
Sbjct: 319 KLGIIGAGMMGNGIAHVSAKVGIEVMLLDVSLEAAERGKANVEKLLSKTVSQGRLSEAKK 378

Query: 61  EQVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPI 120
           +++LA I P  D A  L+G DFV+EAV E ++LK  + + AEA    SAV  TNTS+LPI
Sbjct: 379 DEILALIKPTVDYAD-LQGVDFVVEAVFESVDLKGKVTQQAEAQLPESAVFGTNTSTLPI 437

Query: 121 SEIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKD 180
           S +A+  K P   +G+HFF+P   MPLVEI+ G+ TSD  +    + A+ + K  IVV D
Sbjct: 438 SLLANASKRPANFIGIHFFSPVERMPLVEIICGEQTSDAALAKAFDFARQIGKTAIVVND 497

Query: 181 VPGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSV 240
             GFF +R      + GC L+++G+  +  +D+   +++G P+G   + D   L++   V
Sbjct: 498 SLGFFTSRTFGSYFDEGCKLLQEGVDPLL-IDNLG-KQIGMPVGPLTVLDEVSLELMRKV 555

Query: 241 WKAVTARGFKAFPCSSTEK-------LVSQGKLGVKSGSGYYQYPSPGK----------F 283
            +     G  A    ++         +    + G   G G+Y YP  G+          F
Sbjct: 556 NETQKEMGVFATVFDNSHSDAVGNILIKEYNRPGRHYGGGFYDYPEGGEKTIWPGLYELF 615

Query: 284 VRPTLPSTSKKLGRYLISPAVNEVSYLLREGIV-GKDDAEKGCVLGLGLPK---GILSYA 339
           VRP +    + +   L+   V E    L+EG++    D   G +LG+G P    G L + 
Sbjct: 616 VRPEVVLPVEDIKERLLFRQVIEAVKCLQEGVLRSVADGNVGSILGIGAPTWTGGFLQFV 675

Query: 340 DEIGIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377
           +  G++  V    E+ QT G + ++P  LLL    +G+
Sbjct: 676 NGYGVERFVQRARELAQTYG-ERFTPPVLLLEKAAKGE 712



 Score = 92.8 bits (229), Expect = 5e-23
 Identities = 60/172 (34%), Positives = 88/172 (51%), Gaps = 6/172 (3%)

Query: 410 IVLNRPTRYNAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSLTPV 469
           + ++ P   NA+N      +   ++ LE+   +  + I      F AG D+ E     P 
Sbjct: 16  VTMDMPGPVNAMNQLYRETMAATVNRLEQENGLTGVVIASAKSTFFAGGDLNELTDFKPG 75

Query: 470 KAMIASRKFHEV---FMKIQFLTKPVIAVINGLALGGGMELALSADFRVA--SKTAEMGQ 524
                  K         +++ L  PV+A ING ALGGG E+AL+ ++RV   S  A +G 
Sbjct: 76  DEADFQAKIELTKNDLRRLERLPVPVVAAINGAALGGGFEIALACNYRVLLNSPAAVVGL 135

Query: 525 PEINLGLIPGGGGTQRL-SRLSGRKGLELVLTGRRVKAEEAYRLGIVEFLAE 575
           PE++LGL+PGGGG  RL   L   + L L+L G+R+K  EA  LG+V  L E
Sbjct: 136 PEVSLGLLPGGGGIVRLVHHLGLERALPLLLEGKRMKPAEALALGLVNELIE 187


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: 1003
Number of extensions: 55
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: 2
Length of query: 651
Length of database: 715
Length adjustment: 39
Effective length of query: 612
Effective length of database: 676
Effective search space:   413712
Effective search space used:   413712
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