GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ech in Caulobacter crescentus NA1000

Align enoyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate CCNA_03293 CCNA_03293 multifunctional fatty acid oxidation complex subunit alpha FadJ

Query= BRENDA::P07896
         (722 letters)



>lcl|FitnessBrowser__Caulo:CCNA_03293 CCNA_03293 multifunctional
           fatty acid oxidation complex subunit alpha FadJ
          Length = 696

 Score =  519 bits (1337), Expect = e-151
 Identities = 301/700 (43%), Positives = 422/700 (60%), Gaps = 35/700 (5%)

Query: 11  LAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTVKAIVICGANGNFCAGADIHGFSAFT 70
           + ++ L +PPVNA+S  V   ++     A +D  VKAIV+      F AGADI  F    
Sbjct: 20  IGVVTLNSPPVNALSAAVREGLQGAFDAAIADAAVKAIVLICDGKTFIAGADITEFGKAM 79

Query: 71  PGLALGSLVDEIQRYQKPVLAAIQGVALGGGLELALGCHYRIANAKARVGLPEVTLGILP 130
            G +L  + + I+   KPV+AAI G ALGGGLE+AL  +YR+A   A+ GLPEV +G+LP
Sbjct: 80  TGPSLQDVQNVIENSPKPVIAAIHGTALGGGLEVALVANYRVAVPSAKAGLPEVNIGLLP 139

Query: 131 GARGTQLLPRVVGVPVALDLITSGKYLSADEALRLGILDAVVKSDPVEE-AIKFAQKII- 188
           GA GTQ LPR+VGV  AL+++T+G+++ A  A  +G+ D +V+   + E AI FA+ ++ 
Sbjct: 140 GAGGTQRLPRIVGVEKALEMVTTGQHVPAKAAHAMGLFDELVEEGKLREGAIAFAKAVVA 199

Query: 189 -DKPIEPRRIFNKPVPSLPNMDSVFAEAIAKVR-KQYPGVLAPETCVRSIQASVKHPYEV 246
            ++P++  R  N+ V +      +F EA  K   K++ G +APE  ++ I+A+V  P++ 
Sbjct: 200 ENRPLKKVRDLNEKVEAARGKPEIF-EAFRKANAKKFRGFMAPENNIKCIEAAVNLPFDE 258

Query: 247 GIKEEEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQPVSSVGVLGLGT 306
           G+K E KLFM L    Q+ A +Y FFAE+ A K       +       PV  VGV+G GT
Sbjct: 259 GLKAERKLFMELMTGSQSAAQRYVFFAERQAAKIPDVPDDT----PTIPVKKVGVIGAGT 314

Query: 307 MGRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEKEASRAH--QNGQASAKPKLRF 364
           MG GIA++F   GI V  +E+  + L+    II    E  A +    Q+        L  
Sbjct: 315 MGGGIAMNFLNAGIPVTIIEAKQENLERGVGIIRKNYENTAKKGRLTQDDVEKRMALLTP 374

Query: 365 SSSTKELSTVDLVVEAVFEDMNLKKKVFAELSALCKPGAFLCTNTSALNVDDIASSTDRP 424
           S   + L+  D+++EAVFE M +KK+VF +L  + KPGA L TNTS L+VD IA+ T RP
Sbjct: 375 SMEMEALADCDMIIEAVFELMEIKKEVFTKLDKIAKPGAILATNTSYLDVDAIAAVTSRP 434

Query: 425 QLVIGTHFFSPAHVMRLLEVIPSRYSSPTTIATVMSLSKKIGKIGVVVGNCYGFVGNRML 484
           + VIGTHFFSPA+VMRLLE++    +S   IAT M LSK IGK+ V+VG CYGFVGNRML
Sbjct: 435 ESVIGTHFFSPANVMRLLELVRGDKTSKDVIATCMKLSKTIGKVPVLVGVCYGFVGNRML 494

Query: 485 APYYNQGFFLLEEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLTGPSLP 544
           A    +   L+ EG+ P DVD VL +FG  MGPF +SDLAGLD+GW          P+  
Sbjct: 495 AQRQREAQKLILEGAMPWDVDRVLYDFGLPMGPFAMSDLAGLDIGW---------DPAKT 545

Query: 545 PGTPVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLSTFLSQYRE 604
             + VR           ++LCE  R GQK GKG+Y YD+   R  KP P +   +  + E
Sbjct: 546 SSSTVR-----------EVLCEMDRRGQKNGKGFYDYDE--NRNAKPSPVVEEVIRDFAE 592

Query: 605 VHHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLHGYGWPRHKGGPMF 664
              I++R I+ +EILERCLY ++NE  +ILEEG A R   ID+++++GYGWP + GGPMF
Sbjct: 593 KRQIQRREITDQEILERCLYPMVNEGAKILEEGKAIRASDIDIVWINGYGWPVYSGGPMF 652

Query: 665 YAASVGLPTVLEKLQKYYRQNPDIPQLEPSDYLRRLVAQG 704
           +   VGL  VL K+++++ +  D    +PS  L RLVA+G
Sbjct: 653 WGELVGLDKVLAKMKQFHAELGD--DFKPSALLERLVAEG 690


Lambda     K      H
   0.319    0.136    0.405 

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: 1121
Number of extensions: 41
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 722
Length of database: 696
Length adjustment: 39
Effective length of query: 683
Effective length of database: 657
Effective search space:   448731
Effective search space used:   448731
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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