Alignments for a candidate for ech in Caulobacter crescentus NA1000

GapMind for catabolism of small carbon sources

Alignments 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)



>FitnessBrowser__Caulo:CCNA_03293
          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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Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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
the source code
instructions for running GapMind on your computer

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