GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Phaeobacter inhibens BS107

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 GFF1187 PGA1_c12020 fatty acid oxidation complex FadJ subunit alpha

Query= BRENDA::A4YDS4
         (651 letters)



>FitnessBrowser__Phaeo:GFF1187
          Length = 733

 Score =  164 bits (416), Expect = 1e-44
 Identities = 115/395 (29%), Positives = 195/395 (49%), Gaps = 22/395 (5%)

Query: 2   KVTVIGSGVMGHGIAELAAIAGNEVWMNDISTEILQQAMERIKWSLSKLRESGSLKEGVE 61
           K+ V+G+G+MG GIA ++A AG EV + D       +     +  L K  + G +    +
Sbjct: 328 KIGVLGAGMMGAGIALVSAQAGMEVVLIDRDQAAADKGKAYTESYLDKGIKRGKVTADKK 387

Query: 62  QVLARIHPETDQAQALKGSDFVIEAVKEDLELKRTIFRNAEAHASPSAVLATNTSSLPIS 121
           + +      T     LKG D +IEAV ED  +K  + +  EA      + A+NTS+LPI+
Sbjct: 388 EAMLSRITATPDLDHLKGCDLIIEAVFEDPGVKAEMTKKVEAIIPEDCIFASNTSTLPIT 447

Query: 122 EIASVLKSPQRVVGMHFFNPPVLMPLVEIVRGKDTSDEVVKTTAEMAKSMNKETIVVKDV 181
           ++A     P++ +G+HFF+P   M LVEI++G+ T D  V    +  + + K  IVV D 
Sbjct: 448 DLAEASVRPEQFIGIHFFSPVEKMFLVEIIKGEKTGDRAVAKALDYVRQIRKTPIVVNDA 507

Query: 182 PGFFVNRVLLRIMEAGCYLVEKGIASIQEVDSSAIEELGFPMGVFLLADYTGLDIGYSVW 241
             F+ NR ++  +  G  ++ +G+A    +  +A  +LGFP+G   L D T +D+G  + 
Sbjct: 508 RFFYCNRCIIPYVNEGARMITEGVA--PALIDNAARQLGFPVGPIQLTDETSIDLGAKIA 565

Query: 242 KAVTARGFKAFPCSSTEKLV----SQGKLGVKSGSGYYQYPSPG------KFVRPTLPST 291
           +A  A    A+P S+ + L+     QG+LG KS +G++ Y   G      K ++   P  
Sbjct: 566 RATKAAMGDAYPESAADDLIFWMEEQGRLGRKSNAGFFDYDDKGKRQGYWKGMQEKYPLA 625

Query: 292 SK-----KLGRYLISPAVNEVSYLLREGI-VGKDDAEKGCVLGLGLPK---GILSYADEI 342
            +     ++   L+   V E    L EG+ +   + + G +L  G      G LS+ D I
Sbjct: 626 DEQPDLIEVQERLMFAQVLEAVRALEEGVLMDIREGDVGAILAWGFAPWSGGPLSWLDII 685

Query: 343 GIDVVVNTLEEMRQTSGMDHYSPDPLLLSMVKEGK 377
           G        +++    G + ++  PLL  M ++G+
Sbjct: 686 GTPYAAERCDQLTAKYG-ERFTCPPLLREMAEKGQ 719



 Score = 67.0 bits (162), Expect = 3e-15
 Identities = 52/176 (29%), Positives = 82/176 (46%), Gaps = 19/176 (10%)

Query: 419 NAINGDMIREINQALDSLEEREDVRVIAITGQGRVFSAGADVTEFGSLT------PVKAM 472
           N +NG  + +++  +D     + V+ I IT   + F+ G D+     +       P + +
Sbjct: 26  NVLNGQAMIDLDGLVDDALADDAVKGIVITSGKKDFAGGMDLNVLAKMKEDAGDEPARGL 85

Query: 473 IAS-RKFHEVFMKIQFLT---------KPVIAVINGLALGGGMELALSAD--FRVASKTA 520
                K HE   KI+            KPV A + G A+G G+EL LS    F   +  A
Sbjct: 86  FEGIMKMHEGLRKIERAGMDPKTNKGGKPVAAALPGTAVGIGLELPLSTHRIFAADNPKA 145

Query: 521 EMGQPEINLGLIPGGGGTQRLSRLSG-RKGLELVLTGRRVKAEEAYRLGIVEFLAE 575
           ++G PEI +G+ PG GGT RL R  G       +L G+ V  ++A   GI++ + E
Sbjct: 146 KIGLPEIMVGIFPGAGGTTRLVRKMGAMAAAPFLLEGKLVDPKKAKGAGIIDEVVE 201



 Score = 43.1 bits (100), Expect = 4e-08
 Identities = 32/95 (33%), Positives = 46/95 (48%), Gaps = 10/95 (10%)

Query: 300 ISPAVNEVSYLLREGIVGK--DDAEKGCVLGLGLPKGILSYADEIGIDVVVNTLEEMRQT 357
           I P VNE + ++ EG+     D+A +     LG P G +   DE  ID+        +  
Sbjct: 516 IIPYVNEGARMITEGVAPALIDNAARQ----LGFPVGPIQLTDETSIDLGAKIARATKAA 571

Query: 358 SGMDHY---SPDPLLLSMVKEGKLGRKSGQGFHTY 389
            G D Y   + D L+  M ++G+LGRKS  GF  Y
Sbjct: 572 MG-DAYPESAADDLIFWMEEQGRLGRKSNAGFFDY 605


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: 1039
Number of extensions: 57
Number of successful extensions: 8
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: 733
Length adjustment: 39
Effective length of query: 612
Effective length of database: 694
Effective search space:   424728
Effective search space used:   424728
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