Aligments for a candidate for ech in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments 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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Candidates (tab-delimited)
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Rules (tab-delimited)
Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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

GapMind for catabolism of small carbon sources